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PDBsum entry 1ejg

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Plant protein PDB id
1ejg
Jmol
Contents
Protein chain
48 a.a. *
* Residue conservation analysis
HEADER    PLANT PROTEIN                           02-MAR-00   1EJG
TITLE     CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CRAMBIN (PRO22,SER22/LEU25,ILE25);
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: CRAMBIN
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA;
SOURCE   3 ORGANISM_TAXID: 3721;
SOURCE   4 STRAIN: SUBSP. ABYSSINICA
KEYWDS    VALENCE ELECTRON DENSITY, MULTI-SUBSTATE, MULTIPOLE REFINEMENT, PLANT
KEYWDS   2 PROTEIN
EXPDTA    X-RAY DIFFRACTION
AUTHOR    C.JELSCH,M.M.TEETER,V.LAMZIN,V.PICHON-LESME,B.BLESSING,C.LECOMTE
REVDAT   6   05-FEB-14 1EJG    1       ATOM   CONECT
REVDAT   5   13-JUL-11 1EJG    1       VERSN
REVDAT   4   24-FEB-09 1EJG    1       VERSN
REVDAT   3   01-APR-03 1EJG    1       JRNL
REVDAT   2   10-MAY-00 1EJG    1       COMPND ATOM
REVDAT   1   05-APR-00 1EJG    0
JRNL        AUTH   C.JELSCH,M.M.TEETER,V.LAMZIN,V.PICHON-PESME,R.H.BLESSING,
JRNL        AUTH 2 C.LECOMTE
JRNL        TITL   ACCURATE PROTEIN CRYSTALLOGRAPHY AT ULTRA-HIGH RESOLUTION:
JRNL        TITL 2 VALENCE ELECTRON DISTRIBUTION IN CRAMBIN.
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V.  97  3171 2000
JRNL        REFN                   ISSN 0027-8424
JRNL        PMID   10737790
JRNL        DOI    10.1073/PNAS.97.7.3171
REMARK   2
REMARK   2 RESOLUTION.    0.54 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : MOLLY
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.54
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 22.37
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 97.6
REMARK   3   NUMBER OF REFLECTIONS             : 100989
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : 1 REFLECTION OUT OF 20
REMARK   3   R VALUE            (WORKING SET) : 0.090
REMARK   3   FREE R VALUE                     : 0.094
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 11220
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) : 0.54
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 0.57
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 17547
REMARK   3   BIN R VALUE           (WORKING SET) : 0.1970
REMARK   3   BIN FREE R VALUE                    : 0.2050
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.00
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
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            : 340
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 0
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 2.80
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.023
REMARK   3   BOND ANGLES            (DEGREES) : 2.700
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
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  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  : SHELXL97 DICTIONARY
REMARK   3  PARAMETER FILE  2  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3  TOPOLOGY FILE  2   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: SHELX97 FOLLOWED BY MOLLY (N.K.HANSEN &
REMARK   3  P.COPPENS ACTA CRYSTALLOGR. A34, 909-921) REFINEMENT OF ELECTRON
REMARK   3  DENSITY.
REMARK   4
REMARK   4 1EJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-00.
REMARK 100 THE RCSB ID CODE IS RCSB010638.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 31-MAY-97
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 7
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : EMBL/DESY, HAMBURG
REMARK 200  BEAMLINE                       : BW7A
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.54
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : SOFTWARE AT SYNCHROTRON
REMARK 200  DATA SCALING SOFTWARE          : DREAR
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 79868
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.540
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.6
REMARK 200  DATA REDUNDANCY                : 4.500
REMARK 200  R MERGE                    (I) : 0.05500
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.54
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.55
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.14760
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: NULL
REMARK 200 SOFTWARE USED: ALREADY SOLVED
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 30.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN (40 MG/ML IN 80% ETHANOL)
REMARK 280  IS EQUILIBRATED AGAINST 60% ETHANOL. NOT BUFFERED., PH 7, VAPOR
REMARK 280  DIFFUSION, SITTING DROP, TEMPERATURE 293K
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,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        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        9.24900
REMARK 290   SMTRY3   2  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    THR A  39   CA  -  CB  -  CG2 ANGL. DEV. =  -9.8 DEGREES
REMARK 500    ASP A  43   CA  -  CB  -  CG  ANGL. DEV. =  13.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CBN   RELATED DB: PDB
REMARK 900 CRAMBIN AT 130K AND 0.83 A. TWO SEQUENCE FORMS.
REMARK 900 RELATED ID: 1CRN   RELATED DB: PDB
REMARK 900 CRAMBIN AT 1.5 A AND ROOM TEMPERATURE. TWO SEQUENCE FORMS.
REMARK 900 RELATED ID: 1AB1   RELATED DB: PDB
REMARK 900 CRAMBIN AT 150 K IN THE PURE SER22/ILE25 SEQUENCE FORMS.
REMARK 900 RELATED ID: 1CNR   RELATED DB: PDB
REMARK 900 CRAMBIN AT 150K AND 1.05 A RESOLUTION. PURE PRO22/LEU25
REMARK 900 FORM OF CRAMBIN.
DBREF  1EJG A    1    46  UNP    P01542   CRAM_CRAAB       1     46
SEQADV 1EJG SER A   22  UNP  P01542    PRO    22 MICROHETEROGENEITY
SEQADV 1EJG ILE A   25  UNP  P01542    LEU    25 MICROHETEROGENEITY
SEQRES   1 A   46  THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE
SEQRES   2 A   46  ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA LEU CYS
SEQRES   3 A   46  ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR
SEQRES   4 A   46  CYS PRO GLY ASP TYR ALA ASN
HELIX    1   1 SER A    6  LEU A   18  1                                  13
HELIX    2   2 PRO A   22  GLY A   31  1                                  10
SHEET    1   A 2 THR A   2  CYS A   3  0
SHEET    2   A 2 ILE A  33  ILE A  34 -1  O  ILE A  33   N  CYS A   3
SSBOND   1 CYS A    3    CYS A   40                          1555   1555  2.03
SSBOND   2 CYS A    4    CYS A   32                          1555   1555  2.05
SSBOND   3 CYS A   16    CYS A   26                          1555   1555  2.04
CRYST1   40.824   18.498   22.371  90.00  90.47  90.00 P 1 21 1      2
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      0.024495  0.000000  0.000201        0.00000
SCALE2      0.000000  0.054060  0.000000        0.00000
SCALE3      0.000000  0.000000  0.044702        0.00000
      
PROCHECK
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