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PDBsum entry 3ax2

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Top Page protein ligands Protein-protein interface(s) links
Membrane protein/transport protein PDB id
3ax2
Jmol
Contents
Protein chains
70 a.a.
16 a.a.
65 a.a.
14 a.a.
Ligands
PO4 ×2
Waters ×167
HEADER    MEMBRANE PROTEIN/TRANSPORT PROTEIN      28-MAR-11   3AX2
TITLE     CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX: A DISULFIDE-
TITLE    2 TETHERED COMPLEX WITH A NON-OPTIMIZED, LONG LINKER
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG;
COMPND   3 CHAIN: A, C, E, G;
COMPND   4 FRAGMENT: CYTOSOLIC DOMAIN, UNP RESIDUES 59-126;
COMPND   5 SYNONYM: MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN, OUTER
COMPND   6 MITOCHONDRIAL MEMBRANE RECEPTOR TOM20;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL;
COMPND  10 CHAIN: B, D, F, H;
COMPND  11 FRAGMENT: UNP RESIDUES 12-20;
COMPND  12 SYNONYM: ALDH CLASS 2, ALDH-E2, ALDH1;
COMPND  13 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE   3 ORGANISM_COMMON: RAT;
SOURCE   4 ORGANISM_TAXID: 10116;
SOURCE   5 GENE: TOMM20;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1;
SOURCE  11 MOL_ID: 2;
SOURCE  12 SYNTHETIC: YES;
SOURCE  13 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE  14 ORGANISM_COMMON: RAT;
SOURCE  15 ORGANISM_TAXID: 10116;
SOURCE  16 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
KEYWDS    PROTEIN-PROTEIN COMPLEX, MEMBRANE PROTEIN-TRANSPORT PROTEIN COMPLEX
EXPDTA    X-RAY DIFFRACTION
AUTHOR    T.SAITOH,Y.MAITA,D.KOHDA
REVDAT   1   06-JUL-11 3AX2    0
JRNL        AUTH   T.SAITOH,M.IGURA,Y.MIYAZAKI,T.OSE,N.MAITA,D.KOHDA
JRNL        TITL   CRYSTALLOGRAPHIC SNAPSHOTS OF TOM20-MITOCHONDRIAL
JRNL        TITL 2 PRESEQUENCE INTERACTIONS WITH DISULFIDE-STABILIZED PEPTIDES.
JRNL        REF    BIOCHEMISTRY                  V.  50  5487 2011
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   21591667
JRNL        DOI    10.1021/BI200470X
REMARK   2
REMARK   2 RESOLUTION.    1.90 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0109
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 27.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.9
REMARK   3   NUMBER OF REFLECTIONS             : 31052
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.189
REMARK   3   R VALUE            (WORKING SET) : 0.188
REMARK   3   FREE R VALUE                     : 0.218
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1574
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.90
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.95
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2070
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 92.56
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2350
REMARK   3   BIN FREE R VALUE SET COUNT          : 106
REMARK   3   BIN FREE R VALUE                    : 0.3020
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2536
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 10
REMARK   3   SOLVENT ATOMS            : 167
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 24.77
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.02000
REMARK   3    B22 (A**2) : -0.02000
REMARK   3    B33 (A**2) : 0.03000
REMARK   3    B12 (A**2) : -0.01000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.131
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.072
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.295
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.949
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2599 ; 0.028 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3524 ; 2.193 ; 2.017
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   329 ; 5.125 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   115 ;35.021 ;26.522
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   465 ;15.450 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):     8 ;21.821 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   407 ; 0.164 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1936 ; 0.012 ; 0.021
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1643 ; 1.487 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2626 ; 2.430 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):   956 ; 3.915 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   894 ; 6.344 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK   3  POSITIONS U VALUES
REMARK   4
REMARK   4 3AX2 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-11.
REMARK 100 THE RCSB ID CODE IS RCSB029802.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 21-NOV-10
REMARK 200  TEMPERATURE           (KELVIN) : 95
REMARK 200  PH                             : 4.6
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : PHOTON FACTORY
REMARK 200  BEAMLINE                       : AR-NW12A
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.00
REMARK 200  MONOCHROMATOR                  : NUMERICAL LINK TYPE SI(111)
REMARK 200                                   DOUBLE CRYSTAL MONOCHROMATOR,
REMARK 200                                   LIQUID NITROGEN COOLING
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 210
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL
REMARK 200  DATA SCALING SOFTWARE          : HKL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 32732
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.900
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9
REMARK 200  DATA REDUNDANCY                : 5.800
REMARK 200  R MERGE                    (I) : 0.08100
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.93
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 5.70
REMARK 200  R MERGE FOR SHELL          (I) : 0.58700
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 1WT4
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 56.18
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH4.6, 1M AMMONIUM
REMARK 280  DIHYDROGEN PHOSPJATE, 30% PEG 4000, VAPOR DIFFUSION, HANGING
REMARK 280  DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -Y,X-Y,Z+1/3
REMARK 290       3555   -X+Y,-X,Z+2/3
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       32.78033
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       65.56067
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3, 4
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5410 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5450 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 4
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     GLY A    54
REMARK 465     PRO A    55
REMARK 465     LEU A    56
REMARK 465     GLY C    54
REMARK 465     PRO C    55
REMARK 465     LEU C    56
REMARK 465     GLY E    54
REMARK 465     PRO E    55
REMARK 465     LEU E    56
REMARK 465     GLY E    57
REMARK 465     SER E    58
REMARK 465     ASP E    59
REMARK 465     LEU E    60
REMARK 465     LYS E    61
REMARK 465     GLY G    54
REMARK 465     PRO G    55
REMARK 465     LEU G    56
REMARK 465     GLY G    57
REMARK 465     SER G    58
REMARK 465     ASP G    59
REMARK 465     LEU G    60
REMARK 465     GLY H    12
REMARK 465     PRO H    13
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   OE2  GLU A    79     NH1  ARG F    14              1.95
REMARK 500   OE1  GLN E    75     O    HOH E   157              2.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   O    GLY A    84     OH   TYR G    86     1565     1.98
REMARK 500   CD1  LEU D    18     CG2  THR G   113     3654     2.06
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION
REMARK 500    GLU A  78   CB    GLU A  78   CG     -0.152
REMARK 500    TYR C  86   CD1   TYR C  86   CE1     0.113
REMARK 500    GLU E  78   CB    GLU E  78   CG     -0.128
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    LEU A 110   CB  -  CG  -  CD2 ANGL. DEV. = -11.5 DEGREES
REMARK 500    ARG F  14   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    PRO G 115      127.02    -37.50
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3AWR   RELATED DB: PDB
REMARK 900 RELATED ID: 3AX3   RELATED DB: PDB
REMARK 900 RELATED ID: 3AX5   RELATED DB: PDB
DBREF  3AX2 A   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  3AX2 B   12    20  UNP    P11884   ALDH2_RAT       12     20
DBREF  3AX2 C   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  3AX2 D   12    20  UNP    P11884   ALDH2_RAT       12     20
DBREF  3AX2 E   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  3AX2 F   12    20  UNP    P11884   ALDH2_RAT       12     20
DBREF  3AX2 G   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  3AX2 H   12    20  UNP    P11884   ALDH2_RAT       12     20
SEQADV 3AX2 GLY A   54  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 PRO A   55  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 LEU A   56  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 GLY A   57  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 SER A   58  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 TYR B   21  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 ALA B   22  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY B   23  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 SER B   24  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY B   25  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 CYS B   26  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 NH2 B   27  UNP  P11884              AMIDATION
SEQADV 3AX2 GLY C   54  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 PRO C   55  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 LEU C   56  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 GLY C   57  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 SER C   58  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 TYR D   21  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 ALA D   22  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY D   23  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 SER D   24  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY D   25  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 CYS D   26  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 NH2 D   27  UNP  P11884              AMIDATION
SEQADV 3AX2 GLY E   54  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 PRO E   55  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 LEU E   56  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 GLY E   57  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 SER E   58  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 TYR F   21  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 ALA F   22  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY F   23  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 SER F   24  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY F   25  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 CYS F   26  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 NH2 F   27  UNP  P11884              AMIDATION
SEQADV 3AX2 GLY G   54  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 PRO G   55  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 LEU G   56  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 GLY G   57  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 SER G   58  UNP  Q62760              EXPRESSION TAG
SEQADV 3AX2 TYR H   21  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 ALA H   22  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY H   23  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 SER H   24  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 GLY H   25  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 CYS H   26  UNP  P11884              EXPRESSION TAG
SEQADV 3AX2 NH2 H   27  UNP  P11884              AMIDATION
SEQRES   1 A   73  GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL
SEQRES   2 A   73  GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU
SEQRES   3 A   73  LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS
SEQRES   4 A   73  LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN
SEQRES   5 A   73  LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL
SEQRES   6 A   73  PHE GLN MET LEU LEU THR LYS LEU
SEQRES   1 B   16  GLY PRO ARG LEU SER ARG LEU LEU SER TYR ALA GLY SER
SEQRES   2 B   16  GLY CYS NH2
SEQRES   1 C   73  GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL
SEQRES   2 C   73  GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU
SEQRES   3 C   73  LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS
SEQRES   4 C   73  LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN
SEQRES   5 C   73  LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL
SEQRES   6 C   73  PHE GLN MET LEU LEU THR LYS LEU
SEQRES   1 D   16  GLY PRO ARG LEU SER ARG LEU LEU SER TYR ALA GLY SER
SEQRES   2 D   16  GLY CYS NH2
SEQRES   1 E   73  GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL
SEQRES   2 E   73  GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU
SEQRES   3 E   73  LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS
SEQRES   4 E   73  LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN
SEQRES   5 E   73  LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL
SEQRES   6 E   73  PHE GLN MET LEU LEU THR LYS LEU
SEQRES   1 F   16  GLY PRO ARG LEU SER ARG LEU LEU SER TYR ALA GLY SER
SEQRES   2 F   16  GLY CYS NH2
SEQRES   1 G   73  GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL
SEQRES   2 G   73  GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU
SEQRES   3 G   73  LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS
SEQRES   4 G   73  LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN
SEQRES   5 G   73  LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL
SEQRES   6 G   73  PHE GLN MET LEU LEU THR LYS LEU
SEQRES   1 H   16  GLY PRO ARG LEU SER ARG LEU LEU SER TYR ALA GLY SER
SEQRES   2 H   16  GLY CYS NH2
HET    NH2  B  27       1
HET    NH2  D  27       1
HET    NH2  F  27       1
HET    NH2  H  27       1
HET    PO4  B   2       5
HET    PO4  D   1       5
HETNAM     NH2 AMINO GROUP
HETNAM     PO4 PHOSPHATE ION
FORMUL   2  NH2    4(H2 N)
FORMUL   9  PO4    2(O4 P 3-)
FORMUL  11  HOH   *167(H2 O)
HELIX    1   1 GLY A   57  GLN A   83  1                                  27
HELIX    2   2 ASP A   85  VAL A   99  1                                  15
HELIX    3   3 PRO A  103  LEU A  114  1                                  12
HELIX    4   4 PRO A  115  LEU A  126  1                                  12
HELIX    5   5 ARG B   14  GLY B   25  1                                  12
HELIX    6   6 GLY C   57  GLN C   83  1                                  27
HELIX    7   7 ASP C   85  VAL C   99  1                                  15
HELIX    8   8 PRO C  103  LEU C  114  1                                  12
HELIX    9   9 PRO C  115  LYS C  125  1                                  11
HELIX   10  10 PRO D   13  GLY D   25  1                                  13
HELIX   11  11 ALA E   63  GLN E   83  1                                  21
HELIX   12  12 ASP E   85  VAL E   99  1                                  15
HELIX   13  13 PRO E  103  LEU E  114  1                                  12
HELIX   14  14 PRO E  115  LYS E  125  1                                  11
HELIX   15  15 ARG F   14  GLY F   25  1                                  12
HELIX   16  16 ALA G   63  GLN G   83  1                                  21
HELIX   17  17 ASP G   85  VAL G   99  1                                  15
HELIX   18  18 PRO G  103  GLN G  112  1                                  10
HELIX   19  19 PRO G  115  THR G  124  1                                  10
HELIX   20  20 ARG H   14  GLY H   25  1                                  12
SSBOND   1 CYS A  100    CYS B   26                          1555   1555  2.02
SSBOND   2 CYS C  100    CYS D   26                          1555   1555  2.02
SSBOND   3 CYS E  100    CYS F   26                          1555   1555  2.05
SSBOND   4 CYS G  100    CYS H   26                          1555   1555  2.05
LINK         C   CYS B  26                 N   NH2 B  27     1555   1555  1.48
LINK         C   CYS D  26                 N   NH2 D  27     1555   1555  1.49
LINK         C   CYS F  26                 N   NH2 F  27     1555   1555  1.37
LINK         C   CYS H  26                 N   NH2 H  27     1555   1555  1.25
CISPEP   1 GLY B   12    PRO B   13          0        -1.61
CISPEP   2 GLY F   12    PRO F   13          0        10.05
SITE     1 AC1  5 LYS A  68  GLY B  12  ARG B  14  ARG B  17
SITE     2 AC1  5 HOH B 167
SITE     1 AC2  3 LYS C  68  GLY D  12  ARG D  17
CRYST1   61.490   61.490   98.341  90.00  90.00 120.00 P 31         12
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.016263  0.009389  0.000000        0.00000
SCALE2      0.000000  0.018779  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010169        0.00000
      
PROCHECK
Go to PROCHECK summary
 References

 

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