HEADER CHAPERONE 01-MAR-24 8YJG TITLE CRYSTAL STRUCTURE OF THE NUCLEOTIDE-BINDING DOMAIN OF CANDIDA GLABRATA TITLE 2 HSP90 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT MOLECULAR CHAPERONE HSC82; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE NUCLEOTIDE-BINDING DOMAIN OF C.G. HSP90. THE N- COMPND 6 TERMINAL GSAMGS IS A LINKER SEQUENCE FOR THE N-TERMINAL CLEAVABLE COMPND 7 HIS-TAG FUSION ORIGINATING FROM THE PLASMID. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA GLABRATA; SOURCE 3 ORGANISM_COMMON: NAKASEOMYCES GLABRATUS; SOURCE 4 ORGANISM_TAXID: 5478; SOURCE 5 GENE: HSP90; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS2-THR KEYWDS HSP90, ATPASE, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR L.TAN,X.LI,G.ZHANG,L.CHEN,Y.J.IM REVDAT 2 24-SEP-25 8YJG 1 JRNL REVDAT 1 05-MAR-25 8YJG 0 JRNL AUTH L.TAN,X.LI,G.ZHANG,L.CHEN,Y.J.IM JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF CANDIDA JRNL TITL 2 GLABRATA HSP90 JRNL REF BIODESIGN V. 12 13 2024 JRNL REFN ESSN 2288-7105 JRNL DOI 10.34184/KSSB.2024.12.2.13 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 24255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 30.5700 - 4.5800 0.93 1638 146 0.2252 0.2186 REMARK 3 2 4.5700 - 3.6300 0.99 1636 148 0.1741 0.1865 REMARK 3 3 3.6300 - 3.1700 1.00 1625 146 0.1920 0.2197 REMARK 3 4 3.1700 - 2.8800 1.00 1616 145 0.2054 0.2317 REMARK 3 5 2.8800 - 2.6800 1.00 1587 142 0.2145 0.2249 REMARK 3 6 2.6800 - 2.5200 1.00 1593 143 0.2112 0.2244 REMARK 3 7 2.5200 - 2.3900 1.00 1580 142 0.2078 0.2581 REMARK 3 8 2.3900 - 2.2900 1.00 1594 142 0.2069 0.2481 REMARK 3 9 2.2900 - 2.2000 1.00 1564 139 0.2079 0.2520 REMARK 3 10 2.2000 - 2.1300 1.00 1577 142 0.2072 0.2362 REMARK 3 11 2.1300 - 2.0600 1.00 1561 141 0.1976 0.2609 REMARK 3 12 2.0600 - 2.0000 1.00 1568 140 0.2006 0.2735 REMARK 3 13 2.0000 - 1.9500 1.00 1562 141 0.2221 0.2851 REMARK 3 14 1.9500 - 1.9000 0.99 1557 140 0.2299 0.2719 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.195 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.691 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.32 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 1708 REMARK 3 ANGLE : 0.883 2301 REMARK 3 CHIRALITY : 0.054 266 REMARK 3 PLANARITY : 0.006 295 REMARK 3 DIHEDRAL : 14.339 648 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 8YJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5, 70% (V/V) 2-METHYL REMARK 280 -2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 54.32850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.49275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.16425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.32850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.16425 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 81.49275 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 446 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 469 LIES ON A SPECIAL POSITION. 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 GLY A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 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 ASP A 51 70.00 -160.47 REMARK 500 GLU A 58 89.90 -163.22 REMARK 500 SER A 79 40.50 -98.17 REMARK 500 ILE A 95 -80.97 -127.84 REMARK 500 ALA A 96 35.06 30.01 REMARK 500 HIS A 196 23.80 -140.53 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8YJG A 2 212 UNP A0A0W0DX49_CANGB DBREF2 8YJG A A0A0W0DX49 2 212 SEQADV 8YJG GLY A -4 UNP A0A0W0DX4 EXPRESSION TAG SEQADV 8YJG SER A -3 UNP A0A0W0DX4 EXPRESSION TAG SEQADV 8YJG ALA A -2 UNP A0A0W0DX4 EXPRESSION TAG SEQADV 8YJG MET A -1 UNP A0A0W0DX4 EXPRESSION TAG SEQADV 8YJG GLY A 0 UNP A0A0W0DX4 EXPRESSION TAG SEQADV 8YJG SER A 1 UNP A0A0W0DX4 EXPRESSION TAG SEQRES 1 A 217 GLY SER ALA MET GLY SER SER GLU THR PHE GLU PHE GLN SEQRES 2 A 217 ALA GLU ILE THR GLN LEU MET SER LEU ILE ILE ASN THR SEQRES 3 A 217 VAL TYR SER ASN LYS GLU ILE PHE LEU ARG GLU LEU ILE SEQRES 4 A 217 SER ASN ALA SER ASP ALA ILE ASP LYS ILE ARG TYR GLN SEQRES 5 A 217 ALA LEU SER ASP PRO LYS GLN LEU GLU THR GLU PRO GLU SEQRES 6 A 217 LEU PHE ILE ARG ILE THR PRO ARG PRO GLU GLU LYS VAL SEQRES 7 A 217 LEU GLU ILE ARG ASP SER GLY ILE GLY MET THR LYS ALA SEQRES 8 A 217 GLU LEU ILE ASN ASN LEU GLY THR ILE ALA LYS SER GLY SEQRES 9 A 217 THR LYS ALA PHE MET GLU ALA LEU SER ALA GLY ALA ASP SEQRES 10 A 217 VAL SER MET ILE GLY GLN PHE GLY VAL GLY PHE TYR SER SEQRES 11 A 217 LEU PHE LEU VAL ALA ASP ARG VAL GLN VAL ILE SER LYS SEQRES 12 A 217 ASN ASN ASP ASP GLU GLN TYR ILE TRP GLU SER ASN ALA SEQRES 13 A 217 GLY GLY SER PHE THR VAL THR LEU ASP THR VAL ASN GLU SEQRES 14 A 217 LYS ILE GLY ARG GLY THR ILE LEU ARG LEU PHE MET LYS SEQRES 15 A 217 GLU ASP GLN LEU GLU TYR LEU GLU GLU LYS ARG ILE LYS SEQRES 16 A 217 GLU VAL VAL LYS LYS HIS SER GLU PHE VAL ALA TYR PRO SEQRES 17 A 217 ILE GLN LEU MET VAL THR LYS GLU VAL FORMUL 2 HOH *176(H2 O) HELIX 1 AA1 GLN A 8 THR A 21 1 14 HELIX 2 AA2 GLU A 27 SER A 50 1 24 HELIX 3 AA3 ASP A 51 GLU A 58 5 8 HELIX 4 AA4 PRO A 69 GLU A 71 5 3 HELIX 5 AA5 THR A 84 GLY A 93 1 10 HELIX 6 AA6 LYS A 97 GLY A 110 1 14 HELIX 7 AA7 ASP A 112 GLY A 120 5 9 HELIX 8 AA8 VAL A 121 LEU A 128 5 8 HELIX 9 AA9 GLU A 178 LEU A 184 5 7 HELIX 10 AB1 GLU A 185 LYS A 195 1 11 SHEET 1 AA1 8 GLU A 3 GLU A 6 0 SHEET 2 AA1 8 SER A 154 LEU A 159 -1 O PHE A 155 N PHE A 5 SHEET 3 AA1 8 TYR A 145 SER A 149 -1 N ILE A 146 O THR A 158 SHEET 4 AA1 8 ALA A 130 LYS A 138 -1 N VAL A 135 O TRP A 147 SHEET 5 AA1 8 GLY A 169 MET A 176 -1 O ARG A 173 N GLN A 134 SHEET 6 AA1 8 VAL A 73 ASP A 78 -1 N LEU A 74 O LEU A 174 SHEET 7 AA1 8 ILE A 63 ARG A 68 -1 N ARG A 64 O ARG A 77 SHEET 8 AA1 8 ILE A 204 LEU A 206 1 O GLN A 205 N ILE A 63 CRYST1 73.942 73.942 108.657 90.00 90.00 90.00 P 43 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 0.013524 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009203 0.00000 MASTER 261 0 0 10 8 0 0 6 1860 1 0 17 END