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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
