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- PDB-2v7y: Crystal structure of the molecular chaperone DnaK from Geobacillu... -

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Basic information

Entry
Database: PDB / ID: 2v7y
TitleCrystal structure of the molecular chaperone DnaK from Geobacillus kaustophilus HTA426 in post-ATP hydrolysis state
ComponentsCHAPERONE PROTEIN DNAK
KeywordsCHAPERONE / HSP70 / DNAK / HEAT SHOCK PROTEIN / ATPASE / DOMAIN REARRANGEMENT
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP binding
Similarity search - Function
Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family ...Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Chaperone protein DnaK
Similarity search - Component
Biological speciesGEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsChang, Y.-W. / Sun, Y.-J. / Wang, C. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structures of the 70-kDa Heat Shock Proteins in Domain Disjoining Conformation.
Authors: Chang, Y.-W. / Sun, Y.-J. / Wang, C. / Hsiao, C.-D.
History
DepositionAug 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6724
Polymers55,1251
Non-polymers5463
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.753, 71.455, 183.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHAPERONE PROTEIN DNAK / HEAT SHOCK PROTEIN 70 / HSP70


Mass: 55125.156 Da / Num. of mol.: 1
Fragment: NUCLEOTIDE-BINDING DOMAIN AND SUBSTRATE-BINDING DOMAIN (RESIDUES 1-509)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5KWZ7
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.5
Details: 200 MM AMMONIUM CITRATE, PH 7.5, 20% (V/V) ISOPROPANOL, 15% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
Details: VERTICALLY COLLIMATING PREMIRROR, LN2-COOLED FIXED-EXIT DOUBLE CRYSTAL SI(111) MONOCHROMATOR , TOROIDAL FOCUSING MIRROR
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→29.58 Å / Num. obs: 25994 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 93.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-IceCONTROL SOFTWAREdata reduction
SCALEPACKHKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HSC, 1DKZ

3hsc

1dkz


Resolution: 2.37→29.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 259880.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. RESIDUES GLU46, GLU216, ARG436, LYS464, LYS471, SER472, SER473, SER474, LUE476, GLU478, GLU479, GLU480, ILU481, ARG483, MET484, ILU485, LYS486, GLU487, GLU490, ...Details: BULK SOLVENT MODEL USED. RESIDUES GLU46, GLU216, ARG436, LYS464, LYS471, SER472, SER473, SER474, LUE476, GLU478, GLU479, GLU480, ILU481, ARG483, MET484, ILU485, LYS486, GLU487, GLU490, ASN491, GLU493, ASP495, ARG496, LYS497, ARG498, LYS499, GLU500, GLU503, LEU504 FOR WHICH SIDE CHAIN ELECTRON DENSITY WAS POOR WERE MODELED AS ALANINES. RESIDUES 505-509 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1251 4.8 %RANDOM
Rwork0.227 ---
obs0.227 25994 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3926 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å20 Å20 Å2
2--5.04 Å20 Å2
3----1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.37→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 33 166 3919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.171.5
X-RAY DIFFRACTIONc_mcangle_it4.562
X-RAY DIFFRACTIONc_scbond_it5.432
X-RAY DIFFRACTIONc_scangle_it6.862.5
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 198 5.1 %
Rwork0.309 3708 -
obs--82 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ADP.PARADP.TOP
X-RAY DIFFRACTION5PO4.PARPO4.TOP

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