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- PDB-1am1: ATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE -

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Basic information

Entry
Database: PDB / ID: 1am1
TitleATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE
ComponentsHEAT SHOCK PROTEIN 90Hsp90
KeywordsCHAPERONE / NUCLEOTIDE BINDING SITE
Function / homologyHistidine kinase/HSP90-like ATPase superfamily / HSP90, C-terminal domain / Heat shock hsp90 proteins family signature. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Hsp90 protein / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family ...Histidine kinase/HSP90-like ATPase superfamily / HSP90, C-terminal domain / Heat shock hsp90 proteins family signature. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Hsp90 protein / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family / protein targeting to mitochondrion / protein maturation / box C/D snoRNP assembly / fungal-type cell wall / regulation of telomere maintenance / 'de novo' protein folding / response to osmotic stress / proteasome assembly / positive regulation of telomere maintenance via telomerase / ATPase activity, coupled / unfolded protein binding / cellular response to heat / response to heat / protein stabilization / protein refolding / perinuclear region of cytoplasm / cell surface / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm / ATP-dependent molecular chaperone HSP82
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / 2 Å resolution
AuthorsPearl, L.H. / Roe, S.M. / Prodromou, C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone
Authors: Prodromou, C. / Roe, S.M. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: A Molecular Clamp in the Crystal Structure of the N-Terminal Domain of the Yeast Hsp90 Chaperone
Authors: Prodromou, C. / Roe, S.M. / Piper, P.W. / Pearl, L.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 1997 / Release: Jun 24, 1998
RevisionDateData content typeGroupProviderType
1.0Jun 24, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5052
Polyers24,0771
Non-polymers4271
Water4,017223
1
A: HEAT SHOCK PROTEIN 90
hetero molecules

A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0094
Polyers48,1552
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
γ
α
β
Length a, b, c (Å)73.910, 73.910, 110.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP 43 2 2

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Components

#1: Protein/peptide HEAT SHOCK PROTEIN 90 / Hsp90 / HSP90


Mass: 24077.387 Da / Num. of mol.: 1 / Details: ATP COMPLEX / Fragment: N-TERMINAL
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Genus: Saccharomyces / Plasmid name: PRSETA / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P02829
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 / Density percent sol: 61 %
Crystal growMethod: under oil / pH: 5
Details: PROTEIN WAS CRYSTALLIZED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 27MG/ML PROTEIN, 9.75%(W/V) PEGME 550, 65MM AMMONIUM SULFATE, 32.5MM SODIUM SUCCINATE PH5.0, 5MM ATP AND 5MM MAGNESIUM CHLORIDE., under oil
Crystal grow
*PLUS
Method: unknown
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
136 mg/mlprotein11
23 %mPEG55011
320 mM11CaCl2
410 mMTris-HCl11
55 mMnucleotide11
65 mM11Mg2+

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Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.5 / Synchrotron site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Details: TORROIDAL PT-COATED SI MIRROR / Detector: IMAGE PLATE / Collection date: Jun 1, 1997
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 12.1 Å2 / D resolution high: 2 Å / D resolution low: 24 Å / Number obs: 21414 / Observed criterion sigma I: 2 / Rsym value: 0.116 / NetI over sigmaI: 3.3 / Redundancy: 3.5 % / Percent possible obs: 99.9
Reflection shellHighest resolution: 2 Å / Lowest resolution: 2.05 Å / MeanI over sigI obs: 3 / Rsym value: 0.24 / Redundancy: 3.5 % / Percent possible all: 1
Reflection
*PLUS
Rmerge I obs: 0.116
Reflection shell
*PLUS
Percent possible obs: 1 / Rmerge I obs: 0.24

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLOR3.851phasing
RefineMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1AH6
Details: BULK SOLVENT MODEL USED / R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 23.6 Å2
Least-squares processR factor R work: 0.189 / R factor obs: 0.189 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 20586 / Percent reflection obs: 97.7
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 1689 / Nucleic acid: 0 / Ligand: 27 / Solvent: 223 / Total: 1939
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.98
X-RAY DIFFRACTIONx_mcangle_it2.86
X-RAY DIFFRACTIONx_scbond_it4.02
X-RAY DIFFRACTIONx_scangle_it6.04
Refine LS shellHighest resolution: 2 Å / R factor R work: 0.238 / Lowest resolution: 2.12 Å / Number reflection R work: 3331 / Total number of bins used: 6 / Percent reflection obs: 96.2
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2ADP.PARWATER.TOP
X-RAY DIFFRACTION3WATER.PARADP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68
Refine LS shell
*PLUS
R factor obs: 0.238

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