HEADER CHAPERONE/CHAPERONE INHIBITOR 16-AUG-14 4R3M TITLE CRYSTAL STRUCTURE OF HUMAN HSP90 WITH JR9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 16-223; COMPND 5 SYNONYM: HEAT SHOCK 86 KDA, HSP 86, HSP86, LIPOPOLYSACCHARIDE- COMPND 6 ASSOCIATED PROTEIN 2, LAP-2, LPS-ASSOCIATED PROTEIN 2, RENAL COMPND 7 CARCINOMA ANTIGEN NY-REN-38; COMPND 8 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: HSP90A, HSP90AA1, HSPC1, HSPCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHAPERONE/CHAPERONE INHIBITOR, CHAPERONE-CHAPERONE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,M.YANG,J.REN,B.XIONG,J.HE REVDAT 3 20-MAR-24 4R3M 1 REMARK REVDAT 2 25-NOV-15 4R3M 1 JRNL REVDAT 1 05-NOV-14 4R3M 0 JRNL AUTH J.REN,M.YANG,H.LIU,D.CAO,D.CHEN,J.LI,L.TANG,J.HE,Y.L.CHEN, JRNL AUTH 2 M.GENG,B.XIONG,J.SHEN JRNL TITL MULTI-SUBSTITUTED 8-AMINOIMIDAZO[1,2-A]PYRAZINES BY JRNL TITL 2 GROEBKE-BLACKBURN-BIENAYME REACTION AND THEIR HSP90 JRNL TITL 3 INHIBITORY ACTIVITY. JRNL REF ORG.BIOMOL.CHEM. V. 13 1531 2015 JRNL REFN ISSN 1477-0520 JRNL PMID 25490978 JRNL DOI 10.1039/C4OB01865F REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2022 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 33.4729 - 4.3357 0.99 1977 151 0.1773 0.2089 REMARK 3 2 4.3357 - 3.4425 1.00 1898 151 0.1818 0.1984 REMARK 3 3 3.4425 - 3.0076 1.00 1881 145 0.2234 0.2632 REMARK 3 4 3.0076 - 2.7328 1.00 1888 144 0.2485 0.2448 REMARK 3 5 2.7328 - 2.5370 1.00 1866 145 0.2424 0.2745 REMARK 3 6 2.5370 - 2.3874 1.00 1856 144 0.2335 0.2496 REMARK 3 7 2.3874 - 2.2679 1.00 1855 139 0.2224 0.2511 REMARK 3 8 2.2679 - 2.1692 1.00 1852 154 0.2083 0.2124 REMARK 3 9 2.1692 - 2.0857 1.00 1848 129 0.2111 0.2535 REMARK 3 10 2.0857 - 2.0137 1.00 1848 150 0.2178 0.2531 REMARK 3 11 2.0137 - 1.9508 1.00 1876 125 0.2135 0.2555 REMARK 3 12 1.9508 - 1.8950 1.00 1807 164 0.2102 0.2396 REMARK 3 13 1.8950 - 1.8451 1.00 1863 138 0.2038 0.2330 REMARK 3 14 1.8451 - 1.8001 0.96 1754 143 0.2139 0.2624 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.230 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) : 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 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 : 0.007 1703 REMARK 3 ANGLE : 1.103 2298 REMARK 3 CHIRALITY : 0.079 259 REMARK 3 PLANARITY : 0.004 290 REMARK 3 DIHEDRAL : 15.607 634 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4R3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-13 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 : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.467 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.05500 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) : 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: MOLECULAR REPLACEMENT 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 (%): 61.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 33.28900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.46300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.44700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.28900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.46300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.44700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.28900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.46300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.44700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.28900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.46300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.44700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 124 31.14 -91.58 REMARK 500 ALA A 166 -146.10 62.78 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 JR9 A 301 DBREF 4R3M A 16 224 UNP P07900 HS90A_HUMAN 16 224 SEQRES 1 A 209 GLU VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN SEQRES 2 A 209 LEU MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS SEQRES 3 A 209 GLU ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP SEQRES 4 A 209 ALA LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP PRO SEQRES 5 A 209 SER LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU SEQRES 6 A 209 ILE PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP SEQRES 7 A 209 THR GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN SEQRES 8 A 209 LEU GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET SEQRES 9 A 209 GLU ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY SEQRES 10 A 209 GLN PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA SEQRES 11 A 209 GLU LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU SEQRES 12 A 209 GLN TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR SEQRES 13 A 209 VAL ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR SEQRES 14 A 209 LYS VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR SEQRES 15 A 209 LEU GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS SEQRES 16 A 209 SER GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU SEQRES 17 A 209 LYS HET JR9 A 301 29 HETNAM JR9 N~3~-BENZYL-2-[(6-BROMO-1,3-BENZODIOXOL-5-YL) HETNAM 2 JR9 METHYL]IMIDAZO[1,2-A]PYRAZINE-3,8-DIAMINE FORMUL 2 JR9 C21 H18 BR N5 O2 FORMUL 3 HOH *84(H2 O) HELIX 1 1 GLN A 23 THR A 36 1 14 HELIX 2 2 GLU A 42 ASP A 66 1 25 HELIX 3 3 PRO A 67 ASP A 71 5 5 HELIX 4 4 THR A 99 ASN A 105 1 7 HELIX 5 5 ASN A 105 LEU A 122 1 18 HELIX 6 6 ASP A 127 GLY A 135 5 9 HELIX 7 7 VAL A 136 LEU A 143 5 8 HELIX 8 8 GLN A 194 LEU A 198 5 5 HELIX 9 9 GLU A 199 SER A 211 1 13 SHEET 1 A 8 GLU A 18 ALA A 21 0 SHEET 2 A 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 A 8 GLN A 159 SER A 164 -1 N ALA A 161 O ARG A 173 SHEET 4 A 8 ALA A 145 LYS A 153 -1 N VAL A 150 O TRP A 162 SHEET 5 A 8 GLY A 183 LEU A 190 -1 O ILE A 187 N THR A 149 SHEET 6 A 8 THR A 88 ASP A 93 -1 N ILE A 91 O VAL A 186 SHEET 7 A 8 ILE A 78 ASN A 83 -1 N ASN A 79 O VAL A 92 SHEET 8 A 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 13 ASN A 51 ALA A 55 TYR A 61 ASP A 93 SITE 2 AC1 13 MET A 98 ASN A 106 LEU A 107 ILE A 110 SITE 3 AC1 13 GLY A 135 PHE A 138 TYR A 139 TRP A 162 SITE 4 AC1 13 THR A 184 CRYST1 66.578 90.926 98.894 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 0.015020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010112 0.00000