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- PDB-3a6m: Crystal structure of GrpE from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 3a6m
TitleCrystal structure of GrpE from Thermus thermophilus HB8
ComponentsProtein grpE
KeywordsCHAPERONE / GRPE / COILED-COIL / FOUR-HELIX BUNDLE / DIMER / Stress response
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / protein folding / protein-folding chaperone binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Nucleotide Exchange Factor Grpe; Chain A, domain 2 / Head domain of nucleotide exchange factor GrpE / GrpE nucleotide exchange factor, coiled-coil domain / GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Hemagglutinin Ectodomain; Chain B / Roll ...Nucleotide Exchange Factor Grpe; Chain A, domain 2 / Head domain of nucleotide exchange factor GrpE / GrpE nucleotide exchange factor, coiled-coil domain / GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Hemagglutinin Ectodomain; Chain B / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.23 Å
AuthorsNakamura, A. / Takumi, K. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of a thermophilic GrpE protein: insight into thermosensing function for the DnaK chaperone system
Authors: Nakamura, A. / Takumi, K. / Miki, K.
History
DepositionSep 3, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED.
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein grpE
B: Protein grpE


Theoretical massNumber of molelcules
Total (without water)40,1172
Polymers40,1172
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-55 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.382, 210.382, 210.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-190-

HOH

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Components

#1: Protein Protein grpE / HSP-70 cofactor


Mass: 20058.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1490 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56236
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 9.6712 Å3/Da / Density % sol: 87.2818 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.7M magnesium sulfate, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 26058 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 67.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 54.4
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 10.8 / Num. unique all: 2546 / Rsym value: 0.307 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.23→36.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3689402.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1311 5 %RANDOM
Rwork0.218 ---
obs0.218 26027 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 97.5959 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 118.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.23→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 0 18 2467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it16.651.5
X-RAY DIFFRACTIONc_mcangle_it25.232
X-RAY DIFFRACTIONc_scbond_it42.252
X-RAY DIFFRACTIONc_scangle_it53.652.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.23→3.43 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 186 4.4 %
Rwork0.266 4023 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5ion.paramion.top

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