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- PDB-5obv: Mycoplasma genitalium DnaK deletion mutant lacking SBDalpha in co... -

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Basic information

Entry
Database: PDB / ID: 5obv
TitleMycoplasma genitalium DnaK deletion mutant lacking SBDalpha in complex with ADP and Pi.
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / Complex / co-factor / ATP hydrolysis
Function / homology
Function and homology information


chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP hydrolysis activity / ATP binding / cytosol
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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Chaperone protein DnaK
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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)58,3423
Polymers57,8201
Non-polymers5222
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-17 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.547, 133.547, 64.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 57819.926 Da / Num. of mol.: 1 / Mutation: Polypeptide lacks the last 58 residues.
Source method: isolated from a genetically manipulated source
Details: Contains a C-terminal hexa-histidine tag.
Source: (gene. exp.) Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Gene: dnaK, hsp70, MG305 / Plasmid: pET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47547
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Sodium citrate, PEG MME 5000 and butanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013
RadiationMonochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.49→94.43 Å / Num. obs: 20864 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Net I/σ(I): 17.2
Reflection shellResolution: 2.49→2.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2917 / Rpim(I) all: 0.12 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OBU

5obu


Resolution: 2.49→94.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 30.214 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.575 / ESU R Free: 0.304
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 1009 4.8 %RANDOM
Rwork0.2158 ---
obs0.2182 19811 99.63 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.22 Å2 / Biso mean: 54.721 Å2 / Biso min: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å2-0 Å2-0 Å2
2--2.95 Å2-0 Å2
3----5.91 Å2
Refinement stepCycle: final / Resolution: 2.49→94.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 32 21 4036
Biso mean--43.78 48.7 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194060
X-RAY DIFFRACTIONr_bond_other_d0.0010.023960
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9965487
X-RAY DIFFRACTIONr_angle_other_deg0.8939226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5325.595168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84715776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5821526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
LS refinement shellResolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 62 -
Rwork0.351 1401 -
all-1463 -
obs--96.12 %
Refinement TLS params.Method: refined / Origin x: 37.673 Å / Origin y: 120.0828 Å / Origin z: 68.9535 Å
111213212223313233
T0.0991 Å20.0061 Å20.0008 Å2-0.0778 Å2-0.0323 Å2--0.021 Å2
L0.5741 °20.119 °20.397 °2-0.4122 °2-0.4147 °2--1.0602 °2
S0.0557 Å °-0.0404 Å °-0.0312 Å °-0.0122 Å °-0.0291 Å °0.0309 Å °0.0585 Å °-0.1108 Å °-0.0266 Å °

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