HEADER UNKNOWN FUNCTION 23-JAN-05 1YN4 TITLE CRYSTAL STRUCTURES OF EAP DOMAINS FROM STAPHYLOCOCCUS AUREUS REVEAL AN TITLE 2 UNEXPECTED HOMOLOGY TO BACTERIAL SUPERANTIGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EAPH1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 43-141; 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 STRAIN: MU50; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 DERIVATIVE KEYWDS VIRULENCE FACTOR, TOXIN, EXTRACELLULAR ADHERENCE PROTEIN, KEYWDS 2 STAPHYLOCOCCUS AUREUS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR B.V.GEISBRECHT,B.Y.HAMAOKA,B.PERMAN,A.ZEMLA,D.J.LEAHY REVDAT 4 14-FEB-24 1YN4 1 REMARK SHEET LINK REVDAT 3 24-FEB-09 1YN4 1 VERSN REVDAT 2 17-MAY-05 1YN4 1 JRNL REVDAT 1 01-MAR-05 1YN4 0 JRNL AUTH B.V.GEISBRECHT,B.Y.HAMAOKA,B.PERMAN,A.ZEMLA,D.J.LEAHY JRNL TITL THE CRYSTAL STRUCTURES OF EAP DOMAINS FROM STAPHYLOCOCCUS JRNL TITL 2 AUREUS REVEAL AN UNEXPECTED HOMOLOGY TO BACTERIAL JRNL TITL 3 SUPERANTIGENS. JRNL REF J.BIOL.CHEM. V. 280 17243 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15691839 JRNL DOI 10.1074/JBC.M412311200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 976781.270 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 10167 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) : 0.233 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 507 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1474 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 72 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.08000 REMARK 3 B22 (A**2) : 3.08000 REMARK 3 B33 (A**2) : -6.16000 REMARK 3 B12 (A**2) : 3.82000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 57.95 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ZN.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ZN_TOPH.ION REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 93; NULL REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; NSLS REMARK 200 BEAMLINE : 14-BM-C; X4A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9199; 0.9792, 0.9793, 0.9687 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10167 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, ZINC ACETATE, CACODYLATE, PH REMARK 280 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 46.15333 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 23.07667 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 GLN A 100 CG CD OE1 NE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 LYS A 141 CG CD CE NZ 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 58 -97.58 -107.92 REMARK 500 ARG A 61 66.13 37.03 REMARK 500 ASN A 69 45.69 37.33 REMARK 500 LYS A 120 99.66 -164.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 237 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 45 ND1 REMARK 620 2 GLU A 68 OE2 108.6 REMARK 620 3 HOH A 187 O 71.1 154.8 REMARK 620 4 HOH A 188 O 154.7 75.9 94.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 238 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 84 OE2 REMARK 620 2 ASP A 110 OD2 94.9 REMARK 620 3 HOH A 145 O 96.7 82.6 REMARK 620 4 HOH A 185 O 91.6 169.0 87.9 REMARK 620 5 HOH A 204 O 171.2 80.5 75.3 91.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 237 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 238 DBREF 1YN4 A 43 141 UNP Q99S64 Q99S64_STAAM 43 141 SEQRES 1 A 99 GLY LYS HIS THR VAL PRO TYR THR ILE SER VAL ASP GLY SEQRES 2 A 99 ILE THR ALA LEU HIS ARG THR TYR PHE VAL PHE PRO GLU SEQRES 3 A 99 ASN LYS LYS VAL LEU TYR GLN GLU ILE ASP SER LYS VAL SEQRES 4 A 99 LYS ASN GLU LEU ALA SER GLN ARG GLY VAL THR THR GLU SEQRES 5 A 99 LYS ILE ASN ASN ALA GLN THR ALA THR TYR THR LEU THR SEQRES 6 A 99 LEU ASN ASP GLY ASN LYS LYS VAL VAL ASN LEU LYS LYS SEQRES 7 A 99 ASN ASP ASP ALA LYS ASN SER ILE ASP PRO SER THR ILE SEQRES 8 A 99 LYS GLN ILE GLN ILE VAL VAL LYS HET ZN A 237 1 HET ZN A 238 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *95(H2 O) HELIX 1 1 TYR A 74 GLY A 90 1 17 HELIX 2 2 THR A 92 ASN A 98 1 7 HELIX 3 4 ASP A 129 SER A 131 5 3 SHEET 1 A 3 ILE A 56 THR A 57 0 SHEET 2 A 3 LYS A 44 VAL A 53 -1 N VAL A 53 O ILE A 56 SHEET 3 A 3 THR A 62 PRO A 67 -1 O PHE A 66 N HIS A 45 SHEET 1 B 4 ILE A 56 THR A 57 0 SHEET 2 B 4 LYS A 44 VAL A 53 -1 N VAL A 53 O ILE A 56 SHEET 3 B 4 THR A 101 LEU A 108 -1 N THR A 103 O VAL A 139 SHEET 4 B 4 LYS A 113 ASN A 117 -1 O LYS A 114 N LEU A 106 SHEET 1 C 2 VAL A 72 LEU A 73 0 SHEET 2 C 2 SER A 127 ILE A 128 -1 O ILE A 128 N VAL A 72 LINK ND1 HIS A 45 ZN ZN A 237 1555 1555 2.35 LINK OE2 GLU A 68 ZN ZN A 237 1555 1555 2.45 LINK OE2 GLU A 84 ZN ZN A 238 3665 1555 2.53 LINK OD2 ASP A 110 ZN ZN A 238 1555 1555 2.30 LINK O HOH A 145 ZN ZN A 238 1555 1555 2.76 LINK O HOH A 185 ZN ZN A 238 1555 1555 2.72 LINK O HOH A 187 ZN ZN A 237 1655 1555 2.64 LINK O HOH A 188 ZN ZN A 237 1655 1555 2.61 LINK O HOH A 204 ZN ZN A 238 1555 1555 2.72 SITE 1 AC1 5 HIS A 45 GLU A 68 GLU A 94 HOH A 187 SITE 2 AC1 5 HOH A 188 SITE 1 AC2 6 GLU A 84 ASP A 110 HOH A 145 HOH A 185 SITE 2 AC2 6 HOH A 204 HOH A 208 CRYST1 38.550 38.550 69.230 90.00 90.00 120.00 P 32 3 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 0.025940 0.014977 0.000000 0.00000 SCALE2 0.000000 0.029953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014445 0.00000