HEADER IMMUNE SYSTEM 29-JUL-98 2SPZ TITLE STAPHYLOCOCCAL PROTEIN A, Z-DOMAIN, NMR, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G BINDING PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: Z DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 CELLULAR_LOCATION: CELL WALL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: RV308; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDHZ KEYWDS IMMUNOGLOBULIN-BINDING PROTEIN, THREE-HELICAL BUNDLE STRUCTURE, KEYWDS 2 IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.T.MONTELIONE,M.TASHIRO,R.TEJERO,B.A.LYONS REVDAT 7 22-MAY-24 2SPZ 1 REMARK REVDAT 6 03-NOV-21 2SPZ 1 REMARK SEQADV REVDAT 5 24-FEB-09 2SPZ 1 VERSN REVDAT 4 01-APR-03 2SPZ 1 JRNL REVDAT 3 21-APR-00 2SPZ 1 SPRSDE REVDAT 2 22-DEC-99 2SPZ 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 05-AUG-98 2SPZ 0 SPRSDE 21-APR-00 2SPZ 1SPZ JRNL AUTH M.TASHIRO,R.TEJERO,D.E.ZIMMERMAN,B.CELDA,B.NILSSON, JRNL AUTH 2 G.T.MONTELIONE JRNL TITL HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE Z DOMAIN OF JRNL TITL 2 STAPHYLOCOCCAL PROTEIN A. JRNL REF J.MOL.BIOL. V. 272 573 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9325113 JRNL DOI 10.1006/JMBI.1997.1265 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.JENDEBERG,M.TASHIRO,R.TEJERO,B.A.LYONS,M.UHLEN, REMARK 1 AUTH 2 G.T.MONTELIONE,B.NILSSON REMARK 1 TITL THE MECHANISM OF BINDING STAPHYLOCOCCAL PROTEIN A TO REMARK 1 TITL 2 IMMUNOGLOBIN G DOES NOT INVOLVE HELIX UNWINDING REMARK 1 REF BIOCHEMISTRY V. 35 22 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.TASHIRO,G.T.MONTELIONE REMARK 1 TITL STRUCTURES OF BACTERIAL IMMUNOGLOBULIN-BINDING DOMAINS AND REMARK 1 TITL 2 THEIR COMPLEXES WITH IMMUNOGLOBULIN REMARK 1 REF CURR.OPIN.STRUCT.BIOL. V. 5 471 1995 REMARK 1 REFN ISSN 0959-440X REMARK 1 REFERENCE 3 REMARK 1 AUTH B.A.LYONS,M.TASHIRO,L.CEDERGREN,B.NILSSON,G.T.MONTELIONE REMARK 1 TITL AN IMPROVED STRATEGY FOR DETERMINING RESONANCE ASSIGNMENTS REMARK 1 TITL 2 FOR ISOTOPICALLY ENRICHED PROTEINS AND ITS APPLICATION TO AN REMARK 1 TITL 3 ENGINEERED DOMAIN OF STAPHYLOCOCCAL PROTEIN A REMARK 1 REF BIOCHEMISTRY V. 32 7839 1993 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CONGEN REMARK 3 AUTHORS : BRUCCOLERI,KARPLUS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 2SPZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008044. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 10 MILLIMOLAR K2HPO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SEE REMARKS REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : MODIFIED UNITY 500 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA, CONGEN REMARK 210 METHOD USED : SIMULATED ANNEALING WITH REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST CONFORMATIONAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG REMARK 210 -HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, REMARK 210 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG- REMARK 210 HN(CA)CO, 3D PFG-HCCNH-TOCSY, 3D PFG-HCC (CO)NH-TOCSY, 2D CT 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 2 HIS A 18 NE2 HIS A 18 CD2 -0.066 REMARK 500 3 HIS A 18 NE2 HIS A 18 CD2 -0.068 REMARK 500 6 HIS A 18 NE2 HIS A 18 CD2 -0.066 REMARK 500 7 HIS A 18 NE2 HIS A 18 CD2 -0.068 REMARK 500 8 HIS A 18 NE2 HIS A 18 CD2 -0.067 REMARK 500 9 HIS A 18 NE2 HIS A 18 CD2 -0.066 REMARK 500 10 HIS A 18 NE2 HIS A 18 CD2 -0.068 REMARK 500 REMARK 500 REMARK: NULL 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 1 ARG A 27 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 GLN A 32 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 2 PHE A 5 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 2 PHE A 5 CB - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 PHE A 5 CB - CG - CD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 2 PHE A 30 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 PHE A 30 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 GLN A 32 N - CA - CB ANGL. DEV. = -14.7 DEGREES REMARK 500 3 GLN A 9 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 3 GLN A 9 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 3 PHE A 13 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 3 TYR A 14 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 TYR A 14 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 PHE A 30 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 PHE A 30 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 GLN A 32 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 4 TYR A 14 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 GLN A 32 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 5 GLN A 9 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 5 ARG A 27 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 PHE A 30 CB - CG - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 5 PHE A 30 CB - CG - CD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 6 GLN A 9 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 6 PHE A 30 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 LEU A 44 CB - CG - CD1 ANGL. DEV. = 14.4 DEGREES REMARK 500 7 PHE A 13 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 7 PHE A 13 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 PHE A 30 CB - CG - CD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 7 PHE A 30 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 7 GLN A 32 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 8 TYR A 14 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 8 GLN A 32 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 9 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 9 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 PHE A 30 CB - CG - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 9 PHE A 30 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 10 GLN A 9 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 10 PHE A 13 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 10 TYR A 14 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 10 TYR A 14 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 10 PHE A 30 CB - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 10 PHE A 30 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES 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 1 ASP A 2 -169.25 -71.92 REMARK 500 1 PHE A 5 82.39 -67.68 REMARK 500 1 ASN A 6 -130.24 -109.89 REMARK 500 1 LYS A 7 -106.55 -39.58 REMARK 500 1 ASN A 23 -19.32 -153.35 REMARK 500 1 GLU A 24 -133.04 -73.36 REMARK 500 1 PRO A 38 -83.48 -71.14 REMARK 500 1 ALA A 56 -111.34 -92.62 REMARK 500 2 ASP A 2 -81.41 -39.49 REMARK 500 2 ASN A 3 -60.91 -160.42 REMARK 500 2 LEU A 19 104.72 -58.56 REMARK 500 2 ASN A 21 44.15 -140.64 REMARK 500 3 PHE A 5 -122.75 -86.54 REMARK 500 3 GLU A 8 33.93 -89.90 REMARK 500 3 GLN A 9 -80.61 -44.63 REMARK 500 3 LEU A 19 102.55 -58.33 REMARK 500 3 ALA A 56 -92.11 -90.15 REMARK 500 4 ASP A 2 -109.69 -67.59 REMARK 500 4 ASN A 3 92.25 -160.36 REMARK 500 4 LYS A 4 43.40 -78.27 REMARK 500 4 LYS A 7 -136.97 -90.24 REMARK 500 4 LEU A 19 104.85 -54.25 REMARK 500 4 ASN A 21 30.70 -83.85 REMARK 500 4 ASP A 37 -58.73 -143.70 REMARK 500 4 ALA A 56 -76.05 -91.14 REMARK 500 5 ASP A 2 -157.23 -68.73 REMARK 500 5 PRO A 38 -72.93 -76.28 REMARK 500 6 ASP A 2 -138.19 -84.74 REMARK 500 6 ASN A 6 -53.84 -139.09 REMARK 500 6 LYS A 7 -141.62 -71.94 REMARK 500 6 LEU A 19 96.35 -53.10 REMARK 500 6 ASN A 23 -155.57 -71.82 REMARK 500 6 GLU A 24 -66.60 -90.58 REMARK 500 6 SER A 39 -88.67 -100.24 REMARK 500 7 ASP A 2 -155.85 -85.50 REMARK 500 7 ASN A 6 -155.01 -93.96 REMARK 500 7 LYS A 7 -89.54 -39.01 REMARK 500 7 LEU A 19 100.80 -54.61 REMARK 500 7 PRO A 38 -96.68 -69.02 REMARK 500 8 ASP A 2 -92.82 -65.52 REMARK 500 8 LYS A 7 -84.28 -53.56 REMARK 500 8 ASN A 23 -34.34 -151.50 REMARK 500 8 GLU A 24 -132.66 -75.00 REMARK 500 8 PRO A 38 -92.66 -102.38 REMARK 500 9 ASP A 2 -91.27 -77.68 REMARK 500 9 LYS A 7 -77.77 -55.27 REMARK 500 9 LEU A 22 111.82 -160.02 REMARK 500 9 ASN A 23 2.94 -154.82 REMARK 500 9 GLU A 24 -132.88 -87.16 REMARK 500 9 PRO A 38 -121.02 -97.19 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 1 ARG A 27 0.29 SIDE CHAIN REMARK 500 2 ARG A 27 0.32 SIDE CHAIN REMARK 500 4 ARG A 27 0.29 SIDE CHAIN REMARK 500 5 ARG A 27 0.17 SIDE CHAIN REMARK 500 8 ARG A 27 0.26 SIDE CHAIN REMARK 500 9 ARG A 27 0.20 SIDE CHAIN REMARK 500 10 ARG A 27 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2SPZ A 1 58 UNP P38507 SPA2_STAAU 212 269 SEQADV 2SPZ VAL A 1 UNP P38507 ALA 212 ENGINEERED MUTATION SEQADV 2SPZ ALA A 29 UNP P38507 GLY 240 ENGINEERED MUTATION SEQRES 1 A 58 VAL ASP ASN LYS PHE ASN LYS GLU GLN GLN ASN ALA PHE SEQRES 2 A 58 TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU GLN SEQRES 3 A 58 ARG ASN ALA PHE ILE GLN SER LEU LYS ASP ASP PRO SER SEQRES 4 A 58 GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN SEQRES 5 A 58 ASP ALA GLN ALA PRO LYS HELIX 1 1 ASN A 6 LEU A 19 1 14 HELIX 2 2 GLU A 24 ASP A 37 1 14 HELIX 3 3 GLN A 40 ALA A 56 1 17 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 MODEL 1