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 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 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