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- PDB-6jde: crystal structure of a DNA repair protein -

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Basic information

Entry
Database: PDB / ID: 6jde
Titlecrystal structure of a DNA repair protein
ComponentsPutative DNA repair helicase RadD
KeywordsHYDROLASE / DNA repair protein
Function / homology
Function and homology information


postreplication repair / response to ionizing radiation / helicase activity / double-strand break repair / single-stranded DNA binding / DNA helicase / response to xenobiotic stimulus / translation / cell division / ATP hydrolysis activity ...postreplication repair / response to ionizing radiation / helicase activity / double-strand break repair / single-stranded DNA binding / DNA helicase / response to xenobiotic stimulus / translation / cell division / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc-binding ribosomal protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative DNA repair helicase RadD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYan, X.X. / Tang, Q.
CitationJournal: Proteins / Year: 2019
Title: Crystal structure of a novel ATPase RadD from Escherichia coli.
Authors: Kuang, X. / Tang, Q. / Liu, Y.P. / Yan, X.X. / Xu, W.
History
DepositionFeb 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Putative DNA repair helicase RadD
A: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,1494
Polymers133,0182
Non-polymers1312
Water6,774376
1
B: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5742
Polymers66,5091
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5742
Polymers66,5091
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.515, 78.455, 110.587
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative DNA repair helicase RadD


Mass: 66509.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: radD, yejH, yejI, yejJ, b2184, JW2172 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P33919, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18% PEG3350, 500mM Nacl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 33119 / % possible obs: 97.8 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rrim(I) all: 0.105 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.88 Å / CC1/2: 0.97 / Rrim(I) all: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.953 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.2402 1664 5.05 %
Rwork0.2283 --
obs0.2289 32935 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8620 0 2 376 8998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058875
X-RAY DIFFRACTIONf_angle_d0.96212079
X-RAY DIFFRACTIONf_dihedral_angle_d16.815264
X-RAY DIFFRACTIONf_chiral_restr0.0551359
X-RAY DIFFRACTIONf_plane_restr0.0071585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.88220.35371110.29862171X-RAY DIFFRACTION81
2.8822-2.9750.29591310.29212520X-RAY DIFFRACTION96
2.975-3.08090.30481460.27442622X-RAY DIFFRACTION99
3.0809-3.20380.25441550.25772629X-RAY DIFFRACTION100
3.2038-3.3490.241320.24552637X-RAY DIFFRACTION99
3.349-3.52460.24531230.23252679X-RAY DIFFRACTION100
3.5246-3.74410.23771490.21782654X-RAY DIFFRACTION100
3.7441-4.0310.22421290.20012650X-RAY DIFFRACTION100
4.031-4.43260.18741480.18612641X-RAY DIFFRACTION100
4.4326-5.06480.21691400.19262684X-RAY DIFFRACTION100
5.0648-6.34690.23421650.23292667X-RAY DIFFRACTION100
6.3469-19.95320.23691350.23512717X-RAY DIFFRACTION99

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