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- PDB-4x9l: N-terminal domain of Heat shock protein 90 from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 4x9l
TitleN-terminal domain of Heat shock protein 90 from Oryza sativa
ComponentsHeat shock protein
KeywordsCHAPERONE / Hsp90
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Heat shock protein 81-3 / Heat shock protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRaman, S. / Suguna, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain.
Authors: Raman, S. / Suguna, K.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4653
Polymers27,7651
Non-polymers6992
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-2 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.870, 116.870, 105.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-414-

HOH

31A-420-

HOH

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Components

#1: Protein Heat shock protein


Mass: 27765.096 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Hsp90, Os09g0482400, Os09g0482610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0J0U8, UniProt: Q07078*PLUS
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, PEG 400, Ammonium sulphate / PH range: 7 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953725 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 3.1→58.44 Å / Num. obs: 6890 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKI

2jki


Resolution: 3.1→44.416 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 329 4.78 %
Rwork0.2451 --
obs0.2475 6886 99.85 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.831 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3704 Å2-0 Å2-0 Å2
2--2.3704 Å2-0 Å2
3----4.7408 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 44 20 1641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091647
X-RAY DIFFRACTIONf_angle_d1.4532237
X-RAY DIFFRACTIONf_dihedral_angle_d19.251586
X-RAY DIFFRACTIONf_chiral_restr0.088260
X-RAY DIFFRACTIONf_plane_restr0.005281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.90570.3591600.28443208X-RAY DIFFRACTION100
3.9057-44.42040.26751690.2293349X-RAY DIFFRACTION100

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