PDB Short entry for 1AMX HEADER BACTERIAL ADHESIN 19-JUN-97 1AMX TITLE COLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN ADHESIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CBD (151 - 318); COMPND 5 SYNONYM: CBD19; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: A 19-KDA FRAGMENT OF THE COLLAGEN-BINDING ADHESIN FROM COMPND 8 A STAPHYLOCOCCUS AUREUS (HIS-TAG + RESIDUES 151-318) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: CNA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM101; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PQE-30; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE504; SOURCE 12 EXPRESSION_SYSTEM_GENE: CNA KEYWDS BACTERIAL ADHESIN, MSCRAMM EXPDTA X-RAY DIFFRACTION AUTHOR J.SYMERSKY,S.NARAYANA REVDAT 4 07-FEB-24 1AMX 1 REMARK REVDAT 3 24-FEB-09 1AMX 1 VERSN REVDAT 2 01-APR-03 1AMX 1 JRNL REVDAT 1 24-JUN-98 1AMX 0 JRNL AUTH J.SYMERSKY,J.M.PATTI,M.CARSON,K.HOUSE-POMPEO,M.TEALE, JRNL AUTH 2 D.MOORE,L.JIN,A.SCHNEIDER,L.J.DELUCAS,M.HOOK,S.V.NARAYANA JRNL TITL STRUCTURE OF THE COLLAGEN-BINDING DOMAIN FROM A JRNL TITL 2 STAPHYLOCOCCUS AUREUS ADHESIN. JRNL REF NAT.STRUCT.BIOL. V. 4 833 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9334749 JRNL DOI 10.1038/NSB1097-833 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 11232 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 991 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00 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 : 1208 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : AS IN X-PLOR 3.1 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOL.WAT REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AMX 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_1000171015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN (MSI) REMARK 200 DATA SCALING SOFTWARE : X-GEN (MSI) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12250 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHASES, X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.80000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.90000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.90000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.80000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 139 REMARK 465 ARG A 140 REMARK 465 GLY A 141 REMARK 465 SER A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 147 REMARK 465 HIS A 148 REMARK 465 GLY A 149 REMARK 465 SER A 150 REMARK 465 ILE A 151 REMARK 465 THR A 152 REMARK 465 SER A 153 REMARK 465 GLY A 154 REMARK 465 ASN A 155 REMARK 465 LYS A 156 REMARK 465 SER A 157 REMARK 465 THR A 158 REMARK 465 ASN A 159 REMARK 465 VAL A 160 REMARK 465 THR A 161 REMARK 465 VAL A 162 REMARK 465 HIS A 163 REMARK 465 LYS A 164 REMARK 465 SER A 165 REMARK 465 GLU A 166 REMARK 465 ALA A 167 REMARK 465 GLY A 168 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLY A 178 H2 HOH A 383 1.58 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 SER A 171 111.33 178.20 REMARK 500 HIS A 230 59.83 -117.78 REMARK 500 PHE A 247 70.60 -119.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CBR REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: COLLAGEN-BINDING RESIDUES IDENTIFIED BY SITE REMARK 800 -DIRECTED MUTAGENESIS. DBREF 1AMX A 151 318 UNP Q53654 CNA_STAAU 151 318 SEQRES 1 A 180 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ILE SEQRES 2 A 180 THR SER GLY ASN LYS SER THR ASN VAL THR VAL HIS LYS SEQRES 3 A 180 SER GLU ALA GLY THR SER SER VAL PHE TYR TYR LYS THR SEQRES 4 A 180 GLY ASP MET LEU PRO GLU ASP THR THR HIS VAL ARG TRP SEQRES 5 A 180 PHE LEU ASN ILE ASN ASN GLU LYS SER TYR VAL SER LYS SEQRES 6 A 180 ASP ILE THR ILE LYS ASP GLN ILE GLN GLY GLY GLN GLN SEQRES 7 A 180 LEU ASP LEU SER THR LEU ASN ILE ASN VAL THR GLY THR SEQRES 8 A 180 HIS SER ASN TYR TYR SER GLY GLN SER ALA ILE THR ASP SEQRES 9 A 180 PHE GLU LYS ALA PHE PRO GLY SER LYS ILE THR VAL ASP SEQRES 10 A 180 ASN THR LYS ASN THR ILE ASP VAL THR ILE PRO GLN GLY SEQRES 11 A 180 TYR GLY SER TYR ASN SER PHE SER ILE ASN TYR LYS THR SEQRES 12 A 180 LYS ILE THR ASN GLU GLN GLN LYS GLU PHE VAL ASN ASN SEQRES 13 A 180 SER GLN ALA TRP TYR GLN GLU HIS GLY LYS GLU GLU VAL SEQRES 14 A 180 ASN GLY LYS SER PHE ASN HIS THR VAL HIS ASN FORMUL 2 HOH *124(H2 O) HELIX 1 1 LEU A 219 THR A 221 5 3 HELIX 2 2 ALA A 239 ALA A 246 1 8 HELIX 3 3 GLN A 267 GLY A 270 1 4 SHEET 1 I 5 TYR A 175 ASP A 179 0 SHEET 2 I 5 HIS A 187 ILE A 194 -1 SHEET 3 I 5 ASN A 273 ILE A 283 -1 SHEET 4 I 5 GLN A 215 GLY A 228 -1 SHEET 5 I 5 ASN A 232 TYR A 234 -1 SHEET 1 II 5 LYS A 251 ASP A 255 0 SHEET 2 II 5 THR A 260 ILE A 265 -1 SHEET 3 II 5 ILE A 205 ILE A 211 -1 SHEET 4 II 5 GLU A 290 TYR A 299 -1 SHEET 5 II 5 VAL A 307 HIS A 317 -1 SITE 1 CBR 7 TYR A 175 ARG A 189 PHE A 191 ASN A 193 SITE 2 CBR 7 ASN A 223 TYR A 233 ASN A 278 CRYST1 74.000 74.000 56.700 90.00 90.00 120.00 P 32 2 1 6 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 0.013514 0.007802 0.000000 0.00000 SCALE2 0.000000 0.015604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017637 0.00000