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- PDB-5z68: Structure of the recombination mediator protein RecF-ATP in RecFO... -

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Basic information

Entry
Database: PDB / ID: 5z68
TitleStructure of the recombination mediator protein RecF-ATP 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


DNA synthesis involved in DNA repair / SOS response / double-strand break repair / single-stranded DNA binding / DNA replication / 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
ADENOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / DNA replication and repair protein RecF
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication and repair protein RecF
B: DNA replication and repair protein RecF
C: DNA replication and repair protein RecF
D: DNA replication and repair protein RecF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,13733
Polymers173,5604
Non-polymers3,57729
Water1,874104
1
A: DNA replication and repair protein RecF
B: DNA replication and repair protein RecF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,60317
Polymers86,7802
Non-polymers1,82315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint4 kcal/mol
Surface area32920 Å2
MethodPISA
2
C: DNA replication and repair protein RecF
D: DNA replication and repair protein RecF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,53416
Polymers86,7802
Non-polymers1,75414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-3 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.118, 138.821, 179.567
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
DNA replication and repair protein RecF


Mass: 43389.980 Da / Num. of mol.: 4
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: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.92 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8M ammonium sulfate, 100 mM Tris-Hcl, pH 8.5

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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 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 28.2
Reflection shellResolution: 3→3.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 3→19.863 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.26
RfactorNum. reflection% reflection
Rfree0.2547 2642 4.85 %
Rwork0.1951 --
obs0.198 54453 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11560 0 233 104 11897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112001
X-RAY DIFFRACTIONf_angle_d1.44216132
X-RAY DIFFRACTIONf_dihedral_angle_d17.9184445
X-RAY DIFFRACTIONf_chiral_restr0.0531810
X-RAY DIFFRACTIONf_plane_restr0.0052047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05440.3271530.30012652X-RAY DIFFRACTION100
3.0544-3.11290.3591480.27962687X-RAY DIFFRACTION100
3.1129-3.17620.36661390.27842718X-RAY DIFFRACTION100
3.1762-3.2450.2961290.25492688X-RAY DIFFRACTION100
3.245-3.32010.33881350.23962709X-RAY DIFFRACTION100
3.3201-3.40270.2881380.23042694X-RAY DIFFRACTION100
3.4027-3.49430.30121410.22152710X-RAY DIFFRACTION100
3.4943-3.59650.32191340.21112713X-RAY DIFFRACTION100
3.5965-3.71190.22251340.19532679X-RAY DIFFRACTION100
3.7119-3.84360.26891420.1882710X-RAY DIFFRACTION100
3.8436-3.99630.28371470.18882712X-RAY DIFFRACTION100
3.9963-4.17660.25281220.18412724X-RAY DIFFRACTION100
4.1766-4.39450.22281140.1712753X-RAY DIFFRACTION100
4.3945-4.66650.22391410.15272730X-RAY DIFFRACTION100
4.6665-5.02140.25491380.16932753X-RAY DIFFRACTION100
5.0214-5.51690.23261450.18022759X-RAY DIFFRACTION100
5.5169-6.29290.2831540.21282757X-RAY DIFFRACTION100
6.2929-7.84630.22711440.2112805X-RAY DIFFRACTION100
7.8463-19.86350.20511440.17162858X-RAY DIFFRACTION99

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