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 4 22-MAY-24 1BDD 1 REMARK 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