HEADER CHAPERONE 07-JUN-17 5XQE TITLE CRYSTAL STRUCTURE OF HUMAN HSP90 WITH FS3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 9-236; COMPND 5 SYNONYM: HEAT SHOCK 86 KDA,HSP86,LIPOPOLYSACCHARIDE-ASSOCIATED COMPND 6 PROTEIN 2,LPS-ASSOCIATED PROTEIN 2,RENAL CARCINOMA ANTIGEN NY-REN-38; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HSP90AA1, HSP90A, HSPC1, HSPCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEAT SHOCK PROTEIN HSP 90, INHIBITOR, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,F.SHI,B.XIONG,J.H.HE REVDAT 2 27-MAR-24 5XQE 1 REMARK REVDAT 1 20-JUN-18 5XQE 0 JRNL AUTH J.LI,F.SHI,B.XIONG,J.H.HE JRNL TITL CRYSTAL STRUCTURE OF HUMAN HSP90 WITH FS3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.2_432 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 33081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.8927 - 3.6584 0.99 3309 208 0.1681 0.1550 REMARK 3 2 3.6584 - 2.9043 1.00 3191 204 0.1989 0.2165 REMARK 3 3 2.9043 - 2.5373 1.00 3171 203 0.2086 0.2519 REMARK 3 4 2.5373 - 2.3054 1.00 3146 193 0.1963 0.2070 REMARK 3 5 2.3054 - 2.1402 1.00 3098 208 0.1806 0.2011 REMARK 3 6 2.1402 - 2.0140 0.99 3131 193 0.1824 0.2016 REMARK 3 7 2.0140 - 1.9132 0.99 3101 194 0.1763 0.2241 REMARK 3 8 1.9132 - 1.8299 0.98 3051 183 0.1717 0.2039 REMARK 3 9 1.8299 - 1.7595 0.96 3031 197 0.1859 0.2220 REMARK 3 10 1.7595 - 1.6987 0.93 2878 191 0.1958 0.2304 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 40.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.62190 REMARK 3 B22 (A**2) : 0.32080 REMARK 3 B33 (A**2) : -2.94270 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1691 REMARK 3 ANGLE : 1.022 2282 REMARK 3 CHIRALITY : 0.072 258 REMARK 3 PLANARITY : 0.005 289 REMARK 3 DIHEDRAL : 14.586 633 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 0.4530 30.5845 -20.4522 REMARK 3 T TENSOR REMARK 3 T11: 0.1468 T22: 0.1230 REMARK 3 T33: 0.1462 T12: -0.0061 REMARK 3 T13: -0.0022 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.3645 L22: 0.7042 REMARK 3 L33: 1.3252 L12: -0.3368 REMARK 3 L13: -0.0688 L23: 0.2470 REMARK 3 S TENSOR REMARK 3 S11: -0.0257 S12: -0.0314 S13: -0.0363 REMARK 3 S21: -0.0022 S22: 0.0022 S23: 0.0369 REMARK 3 S31: 0.0792 S32: 0.0276 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300003997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33567 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.699 REMARK 200 RESOLUTION RANGE LOW (A) : 33.886 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25%(W/V) PEG 2000 MONOMETHYL ETHER, REMARK 280 200MM MAGNESIUM CHLORIDE, 100MM SODIUM CACODYLATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 33.88600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.26950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.01600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.88600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.26950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.01600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.88600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.26950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.01600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.88600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.26950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.01600 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 ASP A 9 REMARK 465 GLN A 10 REMARK 465 PRO A 11 REMARK 465 MET A 12 REMARK 465 GLU A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 GLU A 16 REMARK 465 GLU A 225 REMARK 465 ARG A 226 REMARK 465 ASP A 227 REMARK 465 LYS A 228 REMARK 465 GLU A 229 REMARK 465 VAL A 230 REMARK 465 SER A 231 REMARK 465 ASP A 232 REMARK 465 ASP A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 GLU A 236 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 TYR A 38 110.07 -160.41 REMARK 500 ASN A 105 -51.48 -122.74 REMARK 500 ALA A 124 1.05 -66.33 REMARK 500 ALA A 166 -146.16 66.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8CO A 301 DBREF 5XQE A 9 236 UNP P07900 HS90A_HUMAN 9 236 SEQRES 1 A 228 ASP GLN PRO MET GLU GLU GLU GLU VAL GLU THR PHE ALA SEQRES 2 A 228 PHE GLN ALA GLU ILE ALA GLN LEU MET SER LEU ILE ILE SEQRES 3 A 228 ASN THR PHE TYR SER ASN LYS GLU ILE PHE LEU ARG GLU SEQRES 4 A 228 LEU ILE SER ASN SER SER ASP ALA LEU ASP LYS ILE ARG SEQRES 5 A 228 TYR GLU SER LEU THR ASP PRO SER LYS LEU ASP SER GLY SEQRES 6 A 228 LYS GLU LEU HIS ILE ASN LEU ILE PRO ASN LYS GLN ASP SEQRES 7 A 228 ARG THR LEU THR ILE VAL ASP THR GLY ILE GLY MET THR SEQRES 8 A 228 LYS ALA ASP LEU ILE ASN ASN LEU GLY THR ILE ALA LYS SEQRES 9 A 228 SER GLY THR LYS ALA PHE MET GLU ALA LEU GLN ALA GLY SEQRES 10 A 228 ALA ASP ILE SER MET ILE GLY GLN PHE GLY VAL GLY PHE SEQRES 11 A 228 TYR SER ALA TYR LEU VAL ALA GLU LYS VAL THR VAL ILE SEQRES 12 A 228 THR LYS HIS ASN ASP ASP GLU GLN TYR ALA TRP GLU SER SEQRES 13 A 228 SER ALA GLY GLY SER PHE THR VAL ARG THR ASP THR GLY SEQRES 14 A 228 GLU PRO MET GLY ARG GLY THR LYS VAL ILE LEU HIS LEU SEQRES 15 A 228 LYS GLU ASP GLN THR GLU TYR LEU GLU GLU ARG ARG ILE SEQRES 16 A 228 LYS GLU ILE VAL LYS LYS HIS SER GLN PHE ILE GLY TYR SEQRES 17 A 228 PRO ILE THR LEU PHE VAL GLU LYS GLU ARG ASP LYS GLU SEQRES 18 A 228 VAL SER ASP ASP GLU ALA GLU HET 8CO A 301 28 HETNAM 8CO N-[3-[5-CHLORANYL-2,4-BIS(OXIDANYL)PHENYL]-4-(4- HETNAM 2 8CO METHOXYPHENYL)-1,2-OXAZOL-5-YL]-2-METHYL-PROPANAMIDE FORMUL 2 8CO C20 H19 CL N2 O5 FORMUL 3 HOH *114(H2 O) HELIX 1 AA1 GLN A 23 THR A 36 1 14 HELIX 2 AA2 GLU A 42 ASP A 66 1 25 HELIX 3 AA3 PRO A 67 ASP A 71 5 5 HELIX 4 AA4 THR A 99 ASN A 105 1 7 HELIX 5 AA5 ASN A 105 ALA A 124 1 20 HELIX 6 AA6 ASP A 127 GLY A 135 5 9 HELIX 7 AA7 VAL A 136 LEU A 143 5 8 HELIX 8 AA8 GLN A 194 LEU A 198 5 5 HELIX 9 AA9 GLU A 199 SER A 211 1 13 SHEET 1 AA1 8 GLU A 18 ALA A 21 0 SHEET 2 AA1 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 AA1 8 GLN A 159 SER A 164 -1 N ALA A 161 O ARG A 173 SHEET 4 AA1 8 ALA A 145 LYS A 153 -1 N VAL A 150 O TRP A 162 SHEET 5 AA1 8 GLY A 183 LEU A 190 -1 O ILE A 187 N THR A 149 SHEET 6 AA1 8 THR A 88 ASP A 93 -1 N ILE A 91 O VAL A 186 SHEET 7 AA1 8 ILE A 78 ASN A 83 -1 N ILE A 81 O THR A 90 SHEET 8 AA1 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 16 ASN A 51 SER A 52 ALA A 55 LYS A 58 SITE 2 AC1 16 TYR A 61 ASP A 93 ILE A 96 GLY A 97 SITE 3 AC1 16 MET A 98 PHE A 138 THR A 184 VAL A 186 SITE 4 AC1 16 HOH A 404 HOH A 416 HOH A 430 HOH A 436 CRYST1 67.772 90.539 98.032 90.00 90.00 90.00 I 2 2 2 8 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 0.014755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010201 0.00000