HEADER CHAPERONE PROTEIN 19-AUG-16 5LRL
TITLE CRYSTAL STRUCTURE OF HSP90 IN COMPLEX WITH A003492875
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: HEAT SHOCK 86 KDA,HSP86,LIPOPOLYSACCHARIDE-ASSOCIATED
COMPND 5 PROTEIN 2,LPS-ASSOCIATED PROTEIN 2,RENAL CARCINOMA ANTIGEN NY-REN-38;
COMPND 6 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 BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693
KEYWDS CHAPERONE PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR F.VALLEE,A.DUPUY
REVDAT 4 10-JAN-24 5LRL 1 REMARK
REVDAT 3 11-AUG-21 5LRL 1 JRNL
REVDAT 2 12-JUN-19 5LRL 1 AUTHOR JRNL
REVDAT 1 23-AUG-17 5LRL 0
JRNL AUTH S.WOLF,M.AMARAL,M.LOWINSKI,F.VALLEE,D.MUSIL,J.GULDENHAUPT,
JRNL AUTH 2 M.K.DREYER,J.BOMKE,M.FRECH,J.SCHLITTER,K.GERWERT
JRNL TITL ESTIMATION OF PROTEIN-LIGAND UNBINDING KINETICS USING
JRNL TITL 2 NON-EQUILIBRIUM TARGETED MOLECULAR DYNAMICS SIMULATIONS.
JRNL REF J.CHEM.INF.MODEL. V. 59 5135 2019
JRNL REFN ESSN 1549-960X
JRNL PMID 31697501
JRNL DOI 10.1021/ACS.JCIM.9B00592
REMARK 2
REMARK 2 RESOLUTION. 1.33 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.7
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.73
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8
REMARK 3 NUMBER OF REFLECTIONS : 62851
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 + TEST SET) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.174
REMARK 3 FREE R VALUE : 0.189
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940
REMARK 3 FREE R VALUE TEST SET COUNT : 3107
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.36
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.97
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4299
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2110
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4104
REMARK 3 BIN R VALUE (WORKING SET) : 0.2100
REMARK 3 BIN FREE R VALUE : 0.2280
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.54
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 195
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1638
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 354
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.02
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.93
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.38630
REMARK 3 B22 (A**2) : -1.03970
REMARK 3 B33 (A**2) : -1.34660
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.160
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.050
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.050
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.046
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.046
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1707 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 2308 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 609 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 46 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 279 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1707 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 232 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 2345 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.05
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.52
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.74
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5LRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-16.
REMARK 100 THE DEPOSITION ID IS D_1200001245.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-JUN-05
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.934
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63093
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330
REMARK 200 RESOLUTION RANGE LOW (A) : 66.730
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8
REMARK 200 DATA REDUNDANCY : 4.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.38700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 2YJX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 61.62
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 - 1.4M SODIUM CITRATE, 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 33.23000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.35000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.26500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.23000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.35000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.26500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.23000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.35000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.26500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.23000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.35000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.26500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10310 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 ASN A 105 -61.64 -104.68
REMARK 500 ALA A 166 -147.53 63.09
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 73S A 4000
DBREF 5LRL A 16 223 UNP P07900 HS90A_HUMAN 138 345
SEQADV 5LRL HIS A 16 UNP P07900 GLU 138 CLONING ARTIFACT
SEQADV 5LRL MET A 17 UNP P07900 VAL 139 CLONING ARTIFACT
SEQRES 1 A 208 HIS MET GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN
SEQRES 2 A 208 LEU MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS
SEQRES 3 A 208 GLU ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP
SEQRES 4 A 208 ALA LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP PRO
SEQRES 5 A 208 SER LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU
SEQRES 6 A 208 ILE PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP
SEQRES 7 A 208 THR GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN
SEQRES 8 A 208 LEU GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET
SEQRES 9 A 208 GLU ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY
SEQRES 10 A 208 GLN PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA
SEQRES 11 A 208 GLU LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU
SEQRES 12 A 208 GLN TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR
SEQRES 13 A 208 VAL ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR
SEQRES 14 A 208 LYS VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR
SEQRES 15 A 208 LEU GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS
SEQRES 16 A 208 SER GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU
HET 73S A4000 33
HETNAM 73S 2-AZANYL-5-CHLORANYL-~{N}-[(9~{R})-4-(1~{H}-IMIDAZO[4,
HETNAM 2 73S 5-C]PYRIDIN-2-YL)-9~{H}-FLUOREN-9-YL]PYRIMIDINE-4-
HETNAM 3 73S CARBOXAMIDE
FORMUL 2 73S C24 H16 CL N7 O
FORMUL 3 HOH *354(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 GLY A 125 1 21
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 GLU A 192 LEU A 198 5 7
HELIX 9 AA9 GLU A 199 GLN A 212 1 14
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 TYR A 160 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 LEU A 89 O LEU A 188
SHEET 7 AA1 8 ILE A 78 ASN A 83 -1 N ASN A 79 O VAL A 92
SHEET 8 AA1 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80
SITE 1 AC1 18 ASN A 51 ALA A 55 ASP A 93 MET A 98
SITE 2 AC1 18 LEU A 103 ILE A 104 LEU A 107 GLY A 108
SITE 3 AC1 18 GLY A 135 PHE A 138 TYR A 139 TRP A 162
SITE 4 AC1 18 PHE A 170 THR A 184 HOH A4200 HOH A4213
SITE 5 AC1 18 HOH A4281 HOH A4321
CRYST1 66.460 90.700 98.530 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 0.015047 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011025 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010149 0.00000