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PDBsum entry 1ucs

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Antifreeze protein PDB id
1ucs
Jmol
Contents
Protein chain
64 a.a. *
Waters ×240
* Residue conservation analysis
HEADER    ANTIFREEZE PROTEIN                      21-APR-03   1UCS
TITLE     TYPE III ANTIFREEZE PROTEIN RD1 FROM AN ANTARCTIC EEL POUT
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ANTIFREEZE PEPTIDE RD1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: TYPE III ANTIFREEZE PROTEIN RD1
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: LYCODICHTHYS DEARBORNI;
SOURCE   3 ORGANISM_COMMON: ANTARCTIC EEL POUT;
SOURCE   4 ORGANISM_TAXID: 8201
KEYWDS    SMALL BETA BARREL, PRETZEL FOLD, ANTIFREEZE PROTEIN
EXPDTA    X-RAY DIFFRACTION
AUTHOR    T.-P.KO,H.ROBINSON,Y.-G.GAO,C.-H.C.CHENG,A.L.DEVRIES,A.H.-
AUTHOR   2 J.WANG
REVDAT   2   24-FEB-09 1UCS    1       VERSN
REVDAT   1   06-MAY-03 1UCS    0
JRNL        AUTH   T.-P.KO,H.ROBINSON,Y.-G.GAO,C.-H.C.CHENG,
JRNL        AUTH 2 A.L.DEVRIES,A.H.-J.WANG
JRNL        TITL   THE REFINED CRYSTAL STRUCTURE OF AN EEL POUT TYPE
JRNL        TITL 2 III ANTIFREEZE PROTEIN RD1 AT 0.62-(ANGSTROM)
JRNL        TITL 3 RESOLUTION REVEALS STRUCTURAL MICROHETEROGENEITY
JRNL        TITL 4 OF PROTEIN AND SOLVATION
JRNL        REF    BIOPHYS.J.                    V.  84  1228 2003
JRNL        REFN                   ISSN 0006-3495
JRNL        PMID   12547803
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    0.62 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.62
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 22.32
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.8
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.139
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.137
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.155
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 5902
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 127291
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 1020
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 0
REMARK   3   SOLVENT ATOMS      : 240
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL
REMARK   3   NUMBER OF RESTRAINTS                     : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.012
REMARK   3   ANGLE DISTANCES                      (A) : NULL
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: NULL
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: ANISOTROPIC MODEL WAS USED IN
REMARK   3  REFINEMENT AND THEN THE CONVERTED TO ISOTROPIC B VALUES
REMARK   4
REMARK   4 1UCS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-03.
REMARK 100 THE RCSB ID CODE IS RCSB005684.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 23-JAN-00
REMARK 200  TEMPERATURE           (KELVIN) : 110.0
REMARK 200  PH                             : 7.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : APS
REMARK 200  BEAMLINE                       : 19-ID
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.6668
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : CUSTOM-MADE
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 118502
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.620
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.0
REMARK 200  DATA REDUNDANCY                : 3.300
REMARK 200  R MERGE                    (I) : 0.07200
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 21.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.62
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.64
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.8
REMARK 200  DATA REDUNDANCY IN SHELL       : 1.90
REMARK 200  R MERGE FOR SHELL          (I) : 0.65300
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 1.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: A POLYPEPTIDE MODEL DERIVED FROM NMR EXPERIMENTS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 11.58
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL, PH 7.5,
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   X+1/2,-Y+1/2,-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       16.25050
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       22.32000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       19.75100
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       22.32000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       16.25050
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       19.75100
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 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    ASN A   1   CB  -  CA  -  C   ANGL. DEV. =  13.0 DEGREES
REMARK 500    GLU A  35   OE1 -  CD  -  OE2 ANGL. DEV. =  -7.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A 223        DISTANCE =  5.02 ANGSTROMS
REMARK 525    HOH A 236        DISTANCE =  6.74 ANGSTROMS
REMARK 525    HOH A 280        DISTANCE =  9.09 ANGSTROMS
REMARK 525    HOH A 285        DISTANCE =  5.76 ANGSTROMS
REMARK 525    HOH A 300        DISTANCE =  6.91 ANGSTROMS
REMARK 525    HOH A 303        DISTANCE =  8.76 ANGSTROMS
REMARK 525    HOH A 305        DISTANCE =  9.31 ANGSTROMS
REMARK 525    HOH A 321        DISTANCE =  6.83 ANGSTROMS
REMARK 525    HOH A 326        DISTANCE =  5.95 ANGSTROMS
REMARK 525    HOH A 338        DISTANCE =  7.32 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1MSI   RELATED DB: PDB
REMARK 900 HOMOLOGOUS PROTEIN SIMILAR CRYSTAL FORM
REMARK 900 RELATED ID: 1HG7   RELATED DB: PDB
REMARK 900 HOMOLOGOUS PROTEIN SIMILAR CRYSTAL FORM
REMARK 900 RELATED ID: 1OPS   RELATED DB: PDB
REMARK 900 HOMOLOGOUS PROTEIN DIFFERENT CRYSTAL FORM
DBREF  1UCS A    1    64  UNP    P35751   ANP1_RHIDE       1     64
SEQRES   1 A   64  ASN LYS ALA SER VAL VAL ALA ASN GLN LEU ILE PRO ILE
SEQRES   2 A   64  ASN THR ALA LEU THR LEU ILE MET MET LYS ALA GLU VAL
SEQRES   3 A   64  VAL THR PRO MET GLY ILE PRO ALA GLU GLU ILE PRO LYS
SEQRES   4 A   64  LEU VAL GLY MET GLN VAL ASN ARG ALA VAL PRO LEU GLY
SEQRES   5 A   64  THR THR LEU MET PRO ASP MET VAL LYS ASN TYR GLU
FORMUL   2  HOH   *240(H2 O)
HELIX    1   1 THR A   18  ILE A   20  5                                   3
HELIX    2   2 PRO A   33  GLU A   35  5                                   3
HELIX    3   3 GLU A   36  VAL A   41  1                                   6
HELIX    4   4 MET A   56  VAL A   60  5                                   5
SHEET    1   A 2 SER A   4  ALA A   7  0
SHEET    2   A 2 MET A  22  GLU A  25 -1  O  GLU A  25   N  SER A   4
CISPEP   1 THR A   28    PRO A   29          0        -3.23
CRYST1   32.501   39.502   44.640  90.00  90.00  90.00 P 21 21 21    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      0.030768  0.000000  0.000000        0.00000
SCALE2      0.000000  0.025315  0.000000        0.00000
SCALE3      0.000000  0.000000  0.022401        0.00000
      
PROCHECK
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 References