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- PDB-5z69: Structure of the recombination mediator protein RecF-ATPrS in Rec... -

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Basic information

Entry
Database: PDB / ID: 5z69
TitleStructure of the recombination mediator protein RecF-ATPrS 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 / DNA synthesis involved in DNA repair / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA replication and repair protein RecF
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.102 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 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: DNA replication and repair protein RecF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9133
Polymers86,3892
Non-polymers5231
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-11 kcal/mol
Surface area33660 Å2
Unit cell
Length a, b, c (Å)166.727, 48.107, 116.855
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA replication and repair protein RecF


Mass: 43194.734 Da / Num. of mol.: 2
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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 300 mM NaCl, 100 mM Tris-Hcl, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.005 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 913873 / % possible obs: 99.6 % / Redundancy: 7.6 % / Net I/σ(I): 31.2
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.102→19.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.24
RfactorNum. reflection% reflection
Rfree0.2207 2550 4.78 %
Rwork0.1877 --
obs0.1893 53379 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 31 381 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016225
X-RAY DIFFRACTIONf_angle_d1.2678363
X-RAY DIFFRACTIONf_dihedral_angle_d16.972423
X-RAY DIFFRACTIONf_chiral_restr0.051925
X-RAY DIFFRACTIONf_plane_restr0.0051067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1017-2.14210.30711360.25992714X-RAY DIFFRACTION97
2.1421-2.18580.2891470.24592838X-RAY DIFFRACTION99
2.1858-2.23330.32831320.23222757X-RAY DIFFRACTION99
2.2333-2.28510.30311340.22882851X-RAY DIFFRACTION99
2.2851-2.34220.26911400.21552777X-RAY DIFFRACTION99
2.3422-2.40540.22431360.20682810X-RAY DIFFRACTION99
2.4054-2.47610.22641550.20412766X-RAY DIFFRACTION99
2.4761-2.55580.23611430.19852796X-RAY DIFFRACTION99
2.5558-2.6470.23971390.1952812X-RAY DIFFRACTION100
2.647-2.75270.25991400.20022807X-RAY DIFFRACTION100
2.7527-2.87760.27481350.212837X-RAY DIFFRACTION100
2.8776-3.02880.23811610.20272800X-RAY DIFFRACTION100
3.0288-3.21790.25151210.20192877X-RAY DIFFRACTION100
3.2179-3.46510.2361260.18892856X-RAY DIFFRACTION100
3.4651-3.81160.1871570.17172830X-RAY DIFFRACTION100
3.8116-4.3580.1931530.16142871X-RAY DIFFRACTION100
4.358-5.47150.17481410.15852870X-RAY DIFFRACTION100
5.4715-19.83610.20231540.18252960X-RAY DIFFRACTION100
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)
12.4440.21080.15353.6199-0.36762.47980.0211-0.1007-0.05810.18960.0191-0.03830.15790.0042-0.02480.22480.01850.00080.1558-0.0240.2371-37.782-5.03939.2827
25.6564-1.77441.05142.2973-0.42072.2801-0.0270.00570.2330.1630.0257-0.28890.04120.4561-0.05830.2795-0.0368-0.05760.35290.01660.2994-9.4214-2.183515.9304
32.7024-0.4878-0.51041.64840.35861.1967-0.1976-0.83830.53940.54340.12680.0435-0.15840.10820.1060.47950.0243-0.00840.4366-0.10340.2974-30.98764.397324.7004
44.02180.84521.25183.28140.66124.1727-0.0464-0.19040.45740.0715-0.03280.154-0.2238-0.25210.07140.4480.0128-0.18150.3847-0.02710.429522.29843.977553.1471
53.35621.5167-0.7533.3922-2.18134.6911-0.12340.36230.239-0.09070.267-0.0813-0.034-0.0411-0.12390.27890.0593-0.09190.33010.00580.383215.79950.445524.4422
62.21710.41851.72071.71580.37273.29340.308-0.79-0.12370.4981-0.11750.09050.4891-0.9728-0.1620.5034-0.0479-0.07670.61210.04650.38576.6289-7.841147.7638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' AND (RESID -6 THROUGH 114 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 115 THROUGH 257 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 258 THROUGH 365 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID -5 THROUGH 114 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 115 THROUGH 263 )
6X-RAY DIFFRACTION6chain 'B' and (resid 264 through 365 )

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