HEADER CHAPERONE/CHAPERONE INHIBITOR 18-JUN-13 4L90 TITLE CRYSTAL STRUCTURE OF HUMAN HSP90 WITH RL3 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, HSP 86, HSP86, RENAL CARCINOMA ANTIGEN COMPND 6 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATP HYDROLYSIS, HSP90N-HSP90N INHIBITOR COMPLEX, CHAPERONE-CHAPERONE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,J.REN,M.YANG,B.XIONG,J.HE REVDAT 2 08-NOV-23 4L90 1 REMARK REVDAT 1 18-JUN-14 4L90 0 JRNL AUTH J.LI,J.REN,M.YANG,B.XIONG,J.HE JRNL TITL CRYSTAL STRUCTURE OF HUMAN HSP90 WITH RL3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 36.5489 - 4.8188 0.98 1431 153 0.1805 0.2025 REMARK 3 2 4.8188 - 3.8261 0.99 1365 144 0.1470 0.1857 REMARK 3 3 3.8261 - 3.3429 1.00 1348 143 0.1855 0.2112 REMARK 3 4 3.3429 - 3.0374 1.00 1350 144 0.2039 0.2301 REMARK 3 5 3.0374 - 2.8198 1.00 1359 144 0.2000 0.2492 REMARK 3 6 2.8198 - 2.6536 1.00 1334 142 0.2037 0.2149 REMARK 3 7 2.6536 - 2.5207 1.00 1348 143 0.2042 0.2512 REMARK 3 8 2.5207 - 2.4110 1.00 1319 140 0.2009 0.2478 REMARK 3 9 2.4110 - 2.3182 1.00 1348 143 0.1974 0.2454 REMARK 3 10 2.3182 - 2.2382 1.00 1330 141 0.1938 0.2452 REMARK 3 11 2.2382 - 2.1682 1.00 1342 143 0.1923 0.2114 REMARK 3 12 2.1682 - 2.1063 1.00 1329 141 0.1935 0.2271 REMARK 3 13 2.1063 - 2.0508 1.00 1324 140 0.2015 0.2405 REMARK 3 14 2.0508 - 2.0008 0.99 1306 139 0.2385 0.2309 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 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 1698 REMARK 3 ANGLE : 1.098 2294 REMARK 3 CHIRALITY : 0.078 259 REMARK 3 PLANARITY : 0.004 290 REMARK 3 DIHEDRAL : 18.290 640 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 4L90 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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) : 0.9792 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL 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 : 20890 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 36.543 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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) : 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: 3T0Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 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 34.94000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.29400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.99100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.29400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.99100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.29400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.99100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.94000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.29400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.99100 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 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: 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 HOH A 424 O HOH A 473 1.99 REMARK 500 O HOH A 465 O HOH A 476 2.19 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 THR A 94 41.15 -104.28 REMARK 500 ASN A 105 -60.18 -107.07 REMARK 500 ALA A 166 -147.06 60.43 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 RL3 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L8Z RELATED DB: PDB REMARK 900 RELATED ID: 4L91 RELATED DB: PDB REMARK 900 RELATED ID: 4L93 RELATED DB: PDB REMARK 900 RELATED ID: 4L94 RELATED DB: PDB DBREF 4L90 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 RL3 A 301 27 HETNAM RL3 [5-(6-BROMO[1,2,4]TRIAZOLO[4,3-A]PYRIDIN-3-YL)-2,4- HETNAM 2 RL3 DIHYDROXYPHENYL](4-METHYLPIPERAZIN-1-YL)METHANONE FORMUL 2 RL3 C18 H18 BR N5 O3 FORMUL 3 HOH *83(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 ALA A 124 1 20 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 GLU A 192 LEU A 198 5 7 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 TYR A 160 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 ASP A 93 O THR A 184 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 15 ASN A 51 ALA A 55 ASP A 93 ILE A 96 SITE 2 AC1 15 GLY A 97 MET A 98 LEU A 103 LEU A 107 SITE 3 AC1 15 PHE A 138 TRP A 162 THR A 184 HOH A 404 SITE 4 AC1 15 HOH A 408 HOH A 434 HOH A 446 CRYST1 69.880 88.588 97.982 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 0.014310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010206 0.00000