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- PDB-5z67: Structure of the recombination mediator protein RecF in RecFOR pathway -

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Basic information

Entry
Database: PDB / ID: 5z67
TitleStructure of the recombination mediator protein RecF in RecFOR pathway
ComponentsDNA replication and repair protein RecF
KeywordsDNA BINDING PROTEIN / recF / DNA repair / recombination mediator / RecFOR / Rad50
Function / homology
Function and homology information


SOS response / single-stranded DNA binding / DNA replication / DNA repair / ATP binding / cytoplasm
Similarity search - Function
DNA-binding, RecF, conserved site / RecF protein signature 1. / RecF protein signature 2. / DNA-binding, RecF / DNA-binding RecF, domain 2 / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication and repair protein RecF
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTang, Q. / Liu, Y.-P. / Yan, X.-X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400656 China
CitationJournal: Sci Rep / Year: 2018
Title: ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair.
Authors: Tang, Q. / Liu, Y.P. / Shan, H.H. / Tian, L.F. / Zhang, J.Z. / Yan, X.X.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: DNA replication and repair protein RecF


Theoretical massNumber of molelcules
Total (without water)42,5111
Polymers42,5111
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17080 Å2
Unit cell
Length a, b, c (Å)49.839, 95.780, 167.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

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Components

#1: Protein DNA replication and repair protein RecF


Mass: 42511.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: recF, TTE0004
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8RDL3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 28% (w/v) PEG 3350, 300 mM NaCl, 100 mM Tris-Hcl, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / % possible obs: 99 % / Redundancy: 14.5 % / Net I/σ(I): 60.7
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.2→19.992 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.81
RfactorNum. reflection% reflection
Rfree0.2231 1753 8.44 %
Rwork0.1749 --
obs0.1792 20780 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 0 207 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013052
X-RAY DIFFRACTIONf_angle_d1.2624101
X-RAY DIFFRACTIONf_dihedral_angle_d17.7661189
X-RAY DIFFRACTIONf_chiral_restr0.053457
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25950.27661360.19591475X-RAY DIFFRACTION100
2.2595-2.32590.27431310.19241422X-RAY DIFFRACTION100
2.3259-2.40090.23621330.19451442X-RAY DIFFRACTION100
2.4009-2.48650.28091330.20561444X-RAY DIFFRACTION100
2.4865-2.58590.25481340.19761452X-RAY DIFFRACTION100
2.5859-2.70330.26461340.19361451X-RAY DIFFRACTION100
2.7033-2.84540.24391330.20071453X-RAY DIFFRACTION100
2.8454-3.02310.24421340.18481446X-RAY DIFFRACTION100
3.0231-3.25570.2321330.19421456X-RAY DIFFRACTION100
3.2557-3.58160.22371370.16741487X-RAY DIFFRACTION100
3.5816-4.0960.19781350.15461463X-RAY DIFFRACTION100
4.096-5.14590.15741370.14041486X-RAY DIFFRACTION100
5.1459-19.99330.2221430.17171550X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6055-0.1781-0.84234.4358-1.28362.2812-0.2039-0.8206-0.0420.218-0.0147-0.2982-0.11560.42110.20270.1730.0644-0.00360.3633-0.00390.127118.904723.230911.6697
28.13162.91991.48296.173-0.05492.8436-0.029-0.32740.5670.20040.07990.4901-0.5006-0.2139-0.0060.22450.07130.0180.23320.00990.13836.236228.79488.2209
32.0443-1.6654-1.39463.531.87523.10550.02130.09150.0241-0.0103-0.02940.1369-0.0948-0.13170.00360.16420.02320.06710.12640.05910.2103-2.686520.769529.5292
47.9308-8.3358-2.21048.99992.44530.9593-0.49710.2759-1.23920.29640.09971.44440.7105-0.38780.33620.5341-0.01390.19930.32010.01160.4729-10.761411.034332.812
56.75144.49833.23636.56734.10475.77750.183-0.8864-0.49410.3964-0.24150.06180.3158-0.36970.02920.30020.09510.13350.21420.08770.3188-10.29227.054944.0546
60.7218-0.3484-0.011.4938-0.84341.5456-0.135-0.0198-0.26590.16320.00750.16930.22440.15580.10660.23880.05140.12580.19320.00680.31684.69836.577429.3591
71.9466-0.4127-0.41864.4428-0.15151.8993-0.27540.0412-0.56340.0202-0.1751-0.67530.63110.6080.42330.39910.14890.1890.45950.13170.382414.95554.367516.5524
89.81291.6293-1.48552.058-0.1612.6806-0.3469-0.2599-1.0672-0.3732-0.1852-0.58830.73830.6210.4230.44570.19070.13080.380.10960.373122.48798.384210.1983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 216 )
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 240 )
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 263 )
6X-RAY DIFFRACTION6chain 'A' and (resid 264 through 305 )
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 330 )
8X-RAY DIFFRACTION8chain 'A' and (resid 331 through 359 )

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