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PDBsum entry 1wt4

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Protein transport/oxidoreductase PDB id
1wt4
Jmol
Contents
Protein chains
73 a.a.
68 a.a.
13 a.a.
Waters ×152
HEADER    PROTEIN TRANSPORT/OXIDOREDUCTASE        15-NOV-04   1WT4
OBSLTE     12-JUN-07 1WT4      2V1T
TITLE     CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20
COMPND   3 HOMOLOG;
COMPND   4 CHAIN: A, B;
COMPND   5 FRAGMENT: CYTOSOLIC DOMAIN, LIMITED PROTEOLYZED FRAGMENT;
COMPND   6 SYNONYM: MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN,
COMPND   7 OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20;
COMPND   8 ENGINEERED: YES;
COMPND   9 MOL_ID: 2;
COMPND  10 MOLECULE: ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL;
COMPND  11 CHAIN: C, D;
COMPND  12 FRAGMENT: C-TERMINAL HALF OF THE PRESEQUENCE OF
COMPND  13 MITOCHONDRIAL PRECURSOR;
COMPND  14 SYNONYM: ALDH CLASS 2, ALDH1, ALDH-E2;
COMPND  15 EC: 1.2.1.3;
COMPND  16 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE   3 ORGANISM_COMMON: RAT;
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
SOURCE   6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1;
SOURCE   9 MOL_ID: 2;
SOURCE  10 SYNTHETIC: YES;
SOURCE  11 OTHER_DETAILS: ALDH-PRE SEQUENCE
KEYWDS    PROTEIN TRANSPORT
EXPDTA    X-RAY DIFFRACTION
AUTHOR    T.OBITA,M.IGURA,T.OSE,T.ENDO,K.MAENAKA,D.KOHDA
REVDAT   2   12-JUN-07 1WT4    1       OBSLTE
REVDAT   1   22-NOV-05 1WT4    0
JRNL        AUTH   T.OBITA,M.IGURA,T.OSE,T.ENDO,K.MAENAKA,D.KOHDA
JRNL        TITL   CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE
JRNL        TITL 2 COMPLEX
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. 1.90 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 1.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 94.8
REMARK   3   NUMBER OF REFLECTIONS             : 9777
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 SET) : 0.184
REMARK   3   FREE R VALUE                     : 0.242
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : 877
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.90
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.97
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 61.60
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2544
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 0
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1279
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 152
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 19.97
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 23.34
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -5.26600
REMARK   3    B22 (A**2) : 0.59900
REMARK   3    B33 (A**2) : 4.66600
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : -1.70100
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.21
REMARK   3   ESD FROM SIGMAA              (A) : 0.15
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.29
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.24
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.009
REMARK   3   BOND ANGLES            (DEGREES) : 1.51
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 20.45
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.92
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : ISOTROPIC
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST
REMARK   3  SQUARES PROCEDURE
REMARK   4
REMARK   4 1WT4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK   4
REMARK   4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY.
REMARK   4 REMEDIATED DATA FILE REVISION 3.102 (2007-06-08)
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ.
REMARK 100 THE RCSB ID CODE IS RCSB023968.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 04-MAR-2004
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 7.00
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SPRING-8
REMARK 200  BEAMLINE                       : BL40B2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9838
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 9958
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.910
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.9
REMARK 200  DATA REDUNDANCY                : 3.100
REMARK 200  R MERGE                    (I) : 0.06200
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 24.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.98
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.2
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.60
REMARK 200  R MERGE FOR SHELL          (I) : 0.16800
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: AMORE
REMARK 200 STARTING MODEL: 1OM2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 28.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, AMMONIUM CHLORIDE, PH
REMARK 280  7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,1/2+Y,-Z
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 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       13.82200
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 APPLY THE FOLLOWING TO CHAINS: A, C
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 BIOMOLECULE: 2
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B    54
REMARK 465     PRO B    55
REMARK 465     LEU B    56
REMARK 465     GLY B    57
REMARK 465     SER B    58
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: ENGH AND HUBER, 1991
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    CYS A 100   CA  -  CB  -  SG  ANGL. DEV. =  9.7 DEGREES
REMARK 500    LEU B  60   N   -  CA  -  C   ANGL. DEV. =  9.6 DEGREES
REMARK 500    PRO B 117   C   -  N   -  CD  ANGL. DEV. =  9.6 DEGREES
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1OM2   RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE
DBREF  1WT4 A   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  1WT4 B   59   126  UNP    Q62760   TOM20_RAT       59    126
DBREF  1WT4 C   12    22  UNP    P11884   ALDH2_RAT       12     22
DBREF  1WT4 D   12    22  UNP    P11884   ALDH2_RAT       12     22
SEQADV 1WT4 GLY A   54  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 PRO A   55  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 LEU A   56  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 GLY A   57  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 SER A   58  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 MSE A  121  UNP  Q62760    MET   121 MODIFIED RESIDUE
SEQADV 1WT4 GLY B   54  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 PRO B   55  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 LEU B   56  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 GLY B   57  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 SER B   58  UNP  Q62760              CLONING ARTIFACT
SEQADV 1WT4 MSE B  121  UNP  Q62760    MET   121 MODIFIED RESIDUE
SEQADV 1WT4 GLY C   23  UNP  P11884    ALA    23 ENGINEERED
SEQADV 1WT4 CYS C   24  UNP  P11884              CLONING ARTIFACT
SEQADV 1WT4 GLY D   23  UNP  P11884    ALA    23 ENGINEERED
SEQADV 1WT4 CYS D   24  UNP  P11884              CLONING ARTIFACT
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 MSE LEU LEU THR LYS LEU
SEQRES   1 B   73  GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL
SEQRES   2 B   73  GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU
SEQRES   3 B   73  LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS
SEQRES   4 B   73  LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN
SEQRES   5 B   73  LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL
SEQRES   6 B   73  PHE GLN MSE LEU LEU THR LYS LEU
SEQRES   1 C   13  GLY PRO ARG LEU SER ARG LEU LEU SER ALA ALA GLY CYS
SEQRES   1 D   13  GLY PRO ARG LEU SER ARG LEU LEU SER ALA ALA GLY CYS
MODRES 1WT4 MSE A  121  MET  SELENOMETHIONINE
MODRES 1WT4 MSE B  121  MET  SELENOMETHIONINE
HET    MSE  A 121       8
HET    MSE  B 121       8
HETNAM     MSE SELENOMETHIONINE
FORMUL   1  MSE    2(C5 H11 N O2 SE)
FORMUL   5  HOH   *152(H2 O)
HELIX    1   1 ASP A   59  GLY A   84  1                                  26
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 GLU B   64  GLN B   83  1                                  20
HELIX    6   6 ASP B   85  VAL B   99  1                                  15
HELIX    7   7 PRO B  103  LEU B  114  1                                  12
HELIX    8   8 PRO B  115  LYS B  125  1                                  11
HELIX    9   9 LEU B  126  LEU B  126  5                                   1
HELIX   10  10 GLY C   12  ARG C   14  5                                   3
SSBOND   1 CYS A  100    CYS C   24
SSBOND   2 CYS B  100    CYS D   24
CRYST1   33.641   27.644   70.973  90.00 103.06  90.00 P 1 21 1      4
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      0.029726  0.000000  0.006895        0.00000
SCALE2      0.000000  0.036174  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014464        0.00000
      
PROCHECK
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 References