Header list of 1bdd.pdb file
Complete list - 16 202 Bytes
HEADER IMMUNOGLOBULIN-BINDING PROTEIN 28-JUN-96 1BDD
TITLE STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR,
TITLE 2 MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: STAPHYLOCOCCUS AUREUS PROTEIN A;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: B DOMAIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;
SOURCE 3 ORGANISM_TAXID: 1280;
SOURCE 4 GENE: SYNTHETIC GENE;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PPRAFW1
KEYWDS IMMUNOGLOBULIN-BINDING PROTEIN, TRANSMEMBRANE, CELL WALL,
KEYWDS 2 IMMUNOGLOBULIN BINDING DOMAIN
EXPDTA SOLUTION NMR
AUTHOR H.GOUDA,H.TORIGOE,A.SAITO,M.SATO,Y.ARATA,I.SHIMADA
REVDAT 3 16-FEB-22 1BDD 1 REMARK
REVDAT 2 24-FEB-09 1BDD 1 VERSN
REVDAT 1 11-JAN-97 1BDD 0
JRNL AUTH H.GOUDA,H.TORIGOE,A.SAITO,M.SATO,Y.ARATA,I.SHIMADA
JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE B DOMAIN OF
JRNL TITL 2 STAPHYLOCOCCAL PROTEIN A: COMPARISONS OF THE SOLUTION AND
JRNL TITL 3 CRYSTAL STRUCTURES.
JRNL REF BIOCHEMISTRY V. 31 9665 1992
JRNL REFN ISSN 0006-2960
JRNL PMID 1390743
JRNL DOI 10.1021/BI00155A020
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH H.TORIGOE,I.SHIMADA,M.WAELCHLI,A.SAITO,M.SATO,Y.ARATA
REMARK 1 TITL 15N NUCLEAR MAGNETIC RESONANCE STUDIES OF THE B DOMAIN OF
REMARK 1 TITL 2 STAPHYLOCOCCAL PROTEIN A: SEQUENCE SPECIFIC ASSIGNMENTS OF
REMARK 1 TITL 3 THE IMIDE 15N RESONANCES OF THE PROLINE RESIDUES AND THE
REMARK 1 TITL 4 INTERACTION WITH HUMAN IMMUNOGLOBULIN G
REMARK 1 REF FEBS LETT. V. 269 174 1990
REMARK 1 REFN ISSN 0014-5793
REMARK 1 REFERENCE 2
REMARK 1 AUTH H.TORIGOE,I.SHIMADA,A.SAITO,M.SATO,Y.ARATA
REMARK 1 TITL SEQUENTIAL 1H NMR ASSIGNMENTS AND SECONDARY STRUCTURE OF THE
REMARK 1 TITL 2 B DOMAIN OF STAPHYLOCOCCAL PROTEIN A: STRUCTURAL CHANGES
REMARK 1 TITL 3 BETWEEN THE FREE B DOMAIN IN SOLUTION AND THE FC-BOUND B
REMARK 1 TITL 4 DOMAIN IN CRYSTAL
REMARK 1 REF BIOCHEMISTRY V. 29 8787 1990
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 3
REMARK 1 AUTH A.SAITO,S.HONDA,T.NISHI,M.KOIKE,K.OKAZAKI,S.ITOH,M.SATO
REMARK 1 TITL HIGH LEVEL EXPRESSION OF A SYNTHETIC GENE CODING FOR
REMARK 1 TITL 2 IGG-BINDING DOMAIN B OF STAPHYLOCOCCAL PROTEIN A
REMARK 1 REF PROTEIN ENG. V. 2 481 1989
REMARK 1 REFN ISSN 0269-2139
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1BDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000171619.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 5.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; HOHAHA; NOESY; PE
REMARK 210 -COSY; 1H-15N HSQC; DOUBLE-DEPT;
REMARK 210 2D-HMQC-HOHAHA; 2D-HMQC-NOESY;
REMARK 210 HMQC-J
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : JNM-GSX
REMARK 210 SPECTROMETER MANUFACTURER : JEOL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : EMBOSS, X-PLOR
REMARK 210 METHOD USED : HYBRID DISTANCE GEOMETRY
REMARK 210 -DYNAMICAL SIMULATED ANNEALING
REMARK 210 METHOD
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 55
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : AT FIRST, THE DEPOSITORS CARRIED
REMARK 210 OUT THE DISTANCE GEOMETRY
REMARK 210 CALCULATION BY STARTING FROM 55
REMARK 210 INITIAL STRUCTURES. THIS
REMARK 210 CALCULATION RESULTED IN 41
REMARK 210 SOLUTIONS, WHICH HAD CORRECT
REMARK 210 POLYPEPTIDE FOLDS EXCLUDING 14
REMARK 210 MIRROR-IMAGE SUBSTRUCTURES. NEXT,
REMARK 210 THE DYNAMICAL SIMULATED
REMARK 210 ANNEALING CALCULATIONS WERE
REMARK 210 PERFORMED BY USING THESE 41
REMARK 210 SUBSTRUCTURES. THE DISTANCE AND
REMARK 210 TORSION ANGLE VIOLATIONS OF THE
REMARK 210 41 SOLUTIONS OBTAINED BY THE
REMARK 210 DYNAMICAL SIMULATED ANNEALING
REMARK 210 CALCULATIONS WERE SMALLER THAN
REMARK 210 0.6 ANGSTROMS AND 27 DEGREES,
REMARK 210 RESPECTIVELY. THE DEPOSITORS
REMARK 210 SELECTED 10 SOLUTIONS THAT HAD
REMARK 210 THE DISTANCE AND TORSION ANGLE
REMARK 210 VIOLATIONS OF SMALLER THAN 0.5
REMARK 210 ANGSTROMS AND 10 DEGREES,
REMARK 210 RESPECTIVELY.
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 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 HIS A 19 CG HIS A 19 ND1 -0.124
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 ALA A 2 -95.43 45.88
REMARK 500 LYS A 5 53.48 -168.03
REMARK 500 ASN A 7 -38.46 -154.84
REMARK 500 LYS A 8 -26.20 -39.57
REMARK 500 GLU A 9 -25.61 163.64
REMARK 500 GLN A 11 -73.10 -61.86
REMARK 500 PHE A 14 -70.69 -40.15
REMARK 500 ILE A 17 -26.45 -39.82
REMARK 500 LEU A 18 33.07 -80.27
REMARK 500 HIS A 19 -21.59 -145.90
REMARK 500 LEU A 20 94.12 -37.66
REMARK 500 PRO A 39 42.07 -69.68
REMARK 500 ASP A 54 -36.08 -39.84
REMARK 500 LYS A 59 45.80 -83.08
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 28 0.19 SIDE CHAIN
REMARK 500 PHE A 31 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BDC RELATED DB: PDB
DBREF 1BDD A 2 60 UNP P38507 SPA2_STAAU 212 270
SEQRES 1 A 60 THR ALA ASP ASN LYS PHE ASN LYS GLU GLN GLN ASN ALA
SEQRES 2 A 60 PHE TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU
SEQRES 3 A 60 GLN ARG ASN GLY PHE ILE GLN SER LEU LYS ASP ASP PRO
SEQRES 4 A 60 SER GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU
SEQRES 5 A 60 ASN ASP ALA GLN ALA PRO LYS ALA
HELIX 1 1 GLN A 10 HIS A 19 1 10
HELIX 2 2 GLU A 25 ASP A 37 1 13
HELIX 3 3 SER A 42 ALA A 55 1 14
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 16 202 Bytes