HEADER CHAPERONE 11-DEC-25 21FE TITLE NEUTRON CRYSTAL STRUCTURE OF THE ADP BOUND FORM OF THE HUMAN HSP90 N- TITLE 2 TERMINAL DOMAIN 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 OTHER_DETAILS: CELL-FREE SYNTHESIS KEYWDS ATP HYDROLYSIS, PROTEIN FOLDING, CHAPERONE EXPDTA NEUTRON DIFFRACTION AUTHOR Y.HIRANO,K.KUSAKA,T.OSE,K.KURIHARA,K.ABURAI,J.SAITO,T.TAMADA REVDAT 1 03-JUN-26 21FE 0 JRNL AUTH Y.HIRANO,K.KUSAKA,T.OSE,K.KURIHARA,K.ABURAI,J.I.SAITO, JRNL AUTH 2 T.TAMADA JRNL TITL UNPERTURBED HYDRATION STRUCTURE INVOLVES ADP RECOGNITION IN JRNL TITL 2 THE N-TERMINAL DOMAIN OF HUMAN HEAT SHOCK PROTEIN 90 ALPHA. JRNL REF PROTEIN SCI. V. 35 70619 2026 JRNL REFN ESSN 1469-896X JRNL PMID 42148751 JRNL DOI 10.1002/PRO.70619 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 12600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 629 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.17 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2830 REMARK 3 BIN R VALUE (WORKING SET) : 0.2478 REMARK 3 BIN FREE R VALUE : 0.3064 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1679 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.08 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 21FE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300067045. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 14-MAY-24 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : 7.50 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 2.28-6.19 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : IBIX REMARK 230 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 230 DATA SCALING SOFTWARE : NULL REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 12610 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 230 RESOLUTION RANGE LOW (A) : 21.230 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 230 DATA REDUNDANCY : 4.000 REMARK 230 R MERGE (I) : 0.14400 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 7.4000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 230 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 230 DATA REDUNDANCY IN SHELL : 2.60 REMARK 230 R MERGE FOR SHELL (I) : 0.57700 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 1.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 4000, 0.1M HEPES-NAOH PH REMARK 280 7.5, 0.2M MGCL2, 20MM EDTA-NA, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 21.22500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 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: 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 40 51.77 -105.18 REMARK 500 LEU A 70 90.30 -64.94 REMARK 500 ARG A 182 133.47 -35.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 51 OD1 REMARK 620 2 ADP A 301 O3B 93.5 REMARK 620 3 ADP A 301 O2A 91.2 88.1 REMARK 620 4 HOH A 421 O 88.9 176.2 94.9 REMARK 620 5 HOH A 449 O 82.6 86.8 171.7 90.5 REMARK 620 6 HOH A 473 O 174.1 91.9 91.4 85.6 95.3 REMARK 620 N 1 2 3 4 5 DBREF 21FE 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 ADP A 301 40 HET MG A 302 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *115(H2 O) HELIX 1 AA1 GLN A 23 ASN A 35 1 13 HELIX 2 AA2 GLU A 42 ASP A 66 1 25 HELIX 3 AA3 PRO A 67 LEU A 70 5 4 HELIX 4 AA4 THR A 99 LEU A 107 1 9 HELIX 5 AA5 GLY A 114 ALA A 124 1 11 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 SER A 211 1 13 SHEET 1 AA1 8 VAL A 17 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 ILE A 91 O VAL A 186 SHEET 7 AA1 8 ILE A 78 ASN A 83 -1 N ASN A 83 O THR A 88 SHEET 8 AA1 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 LINK OD1 ASN A 51 MG MG A 302 1555 1555 2.08 LINK O3B ADP A 301 MG MG A 302 1555 1555 2.02 LINK O2A ADP A 301 MG MG A 302 1555 1555 2.00 LINK MG MG A 302 O HOH A 421 1555 1555 2.03 LINK MG MG A 302 O HOH A 449 1555 1555 2.23 LINK MG MG A 302 O HOH A 473 1555 1555 2.18 CRYST1 54.120 42.450 54.910 90.00 116.60 90.00 P 1 21 1 2 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 0.018477 0.000000 0.009253 0.00000 SCALE2 0.000000 0.023557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020367 0.00000 CONECT 707 3658 CONECT 3618 3619 3620 3621 3625 CONECT 3619 3618 CONECT 3620 3618 CONECT 3621 3618 3658 CONECT 3622 3623 3624 3625 3626 CONECT 3623 3622 CONECT 3624 3622 3658 CONECT 3625 3618 3622 CONECT 3626 3622 3627 CONECT 3627 3626 3628 3646 3647 CONECT 3628 3627 3629 3630 3648 CONECT 3629 3628 3634 CONECT 3630 3628 3631 3632 3649 CONECT 3631 3630 CONECT 3632 3630 3633 3634 3651 CONECT 3633 3632 CONECT 3634 3629 3632 3635 3653 CONECT 3635 3634 3636 3644 CONECT 3636 3635 3637 3654 CONECT 3637 3636 3638 CONECT 3638 3637 3639 3644 CONECT 3639 3638 3640 3641 CONECT 3640 3639 CONECT 3641 3639 3642 CONECT 3642 3641 3643 3657 CONECT 3643 3642 3644 CONECT 3644 3635 3638 3643 CONECT 3646 3627 CONECT 3647 3627 CONECT 3648 3628 CONECT 3649 3630 CONECT 3651 3632 CONECT 3653 3634 CONECT 3654 3636 CONECT 3657 3642 CONECT 3658 707 3621 3624 3689 CONECT 3658 3761 3815 CONECT 3689 3658 CONECT 3761 3658 CONECT 3815 3658 MASTER 250 0 2 9 8 0 0 6 1822 1 41 18 END