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- PDB-5obx: Mycoplasma genitalium DnaK-NBD -

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Basic information

Entry
Database: PDB / ID: 5obx
TitleMycoplasma genitalium DnaK-NBD
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / Complex / co-factor / ATP hydrolysis
Function / homology
Function and homology information


: / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Chaperone DnaK / 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 70 family / Hsp70 protein / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Chaperone DnaK / 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 70 family / Hsp70 protein / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chaperone protein DnaK
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsAdell, M. / Calisto, B. / Fita, I. / Martinelli, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOBFU2009-09268 Spain
CitationJournal: Protein Sci. / Year: 2018
Title: The nucleotide-bound/substrate-bound conformation of the Mycoplasma genitalium DnaK chaperone.
Authors: Adell, M. / Calisto, B.M. / Fita, I. / Martinelli, L.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,84912
Polymers40,7501
Non-polymers1,09911
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-83 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.921, 157.921, 64.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 40749.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains a C-terminal hexa-histidine tag. / Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: dnaK, hsp70, MG305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47547
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, ammonium sulfate, potassium thiocyanate / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2014
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→78.96 Å / Num. obs: 57432 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.02 / Net I/σ(I): 16
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8302 / Rpim(I) all: 0.36 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OBW

5obw


Resolution: 1.78→45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.756 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20369 2915 5.1 %RANDOM
Rwork0.18162 ---
obs0.18275 54515 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å2-0 Å2
2--0.63 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: 1 / Resolution: 1.78→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 63 225 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192926
X-RAY DIFFRACTIONr_bond_other_d0.0020.022853
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.0023950
X-RAY DIFFRACTIONr_angle_other_deg0.92736643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75225.431116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7821517
X-RAY DIFFRACTIONr_chiral_restr0.090.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7411.7641486
X-RAY DIFFRACTIONr_mcbond_other1.7371.7621485
X-RAY DIFFRACTIONr_mcangle_it2.5992.6351858
X-RAY DIFFRACTIONr_mcangle_other2.62.6371859
X-RAY DIFFRACTIONr_scbond_it3.4322.3961440
X-RAY DIFFRACTIONr_scbond_other3.4332.3961440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1363.3962092
X-RAY DIFFRACTIONr_long_range_B_refined8.71323.4173166
X-RAY DIFFRACTIONr_long_range_B_other8.73523.4333167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 178 -
Rwork0.272 3909 -
obs--95.89 %
Refinement TLS params.Method: refined / Origin x: 10.57 Å / Origin y: -27.979 Å / Origin z: 23.387 Å
111213212223313233
T0.0299 Å20.0102 Å2-0.0346 Å2-0.0198 Å20.014 Å2--0.6543 Å2
L0.5259 °2-0.3993 °20.1317 °2-1.0297 °2-0.3791 °2--0.1419 °2
S-0.0127 Å °-0.0856 Å °0.0401 Å °0.0231 Å °0.0395 Å °-0.052 Å °-0.0089 Å °-0.0182 Å °-0.0268 Å °

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