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- PDB-7r7j: Crystal structure of RadD with ADP -

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Basic information

Entry
Database: PDB / ID: 7r7j
TitleCrystal structure of RadD with ADP
ComponentsPutative DNA repair helicase RadD
KeywordsDNA BINDING PROTEIN / ATPase / SF2
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
ADENOSINE-5'-DIPHOSPHATE / Putative DNA repair helicase RadD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsOsorio Garcia, M.A. / Satyshur, K.A. / Keck, J.L. / Cox, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RM1 GM130450 United States
CitationJournal: Plos One / Year: 2022
Title: X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain.
Authors: Osorio Garcia, M.A. / Satyshur, K.A. / Cox, M.M. / Keck, J.L.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA repair helicase RadD
B: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,18310
Polymers133,0182
Non-polymers1,1658
Water5,152286
1
A: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0915
Polymers66,5091
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative DNA repair helicase RadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0915
Polymers66,5091
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.415, 74.449, 109.400
Angle α, β, γ (deg.)84.659, 80.028, 82.769
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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 (strain K12) (bacteria)
Strain: K12 / Gene: radD, yejH, yejI, yejJ, b2184, JW2172 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K12 / Variant (production host): STL2669(DE3) / References: UniProt: P33919, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 20 mM Tris-HCl, 100 mM potassium chloride, 0.5 mM DTT, 0.5 mM magnesium chloride, 0.5 mM ATPgS, 9% (w/v) PEG 3350, 75 mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.03→45 Å / Num. obs: 79347 / % possible obs: 90.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.066 / Rrim(I) all: 0.124 / Χ2: 0.93 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
4.37-453.60.05412.786470.9930.9980.0340.0640.59498.8
2.03-2.12.11.1050.153210.390.7490.811.3780.77760.7

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.19.1_4122phasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DJE

6dje


Resolution: 2.03→35.65 Å / SU ML: 0.2928 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 33.5395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 1812 2.54 %
Rwork0.2364 69417 -
obs0.2373 71229 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.13 Å2
Refinement stepCycle: LAST / Resolution: 2.03→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8846 0 60 286 9192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039101
X-RAY DIFFRACTIONf_angle_d0.60812372
X-RAY DIFFRACTIONf_chiral_restr0.04171374
X-RAY DIFFRACTIONf_plane_restr0.00471623
X-RAY DIFFRACTIONf_dihedral_angle_d9.15491273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.4371850.36182768X-RAY DIFFRACTION42.37
2.09-2.150.3588970.33113560X-RAY DIFFRACTION53.97
2.15-2.220.35941040.32794192X-RAY DIFFRACTION62.95
2.22-2.30.37131170.30594593X-RAY DIFFRACTION70.39
2.3-2.390.36841380.29775163X-RAY DIFFRACTION78.07
2.39-2.50.32031480.28595437X-RAY DIFFRACTION82.74
2.5-2.630.30431430.28235803X-RAY DIFFRACTION87.16
2.63-2.790.3211560.26235952X-RAY DIFFRACTION90.45
2.79-3.010.2641630.256159X-RAY DIFFRACTION93.87
3.01-3.310.25441650.24956361X-RAY DIFFRACTION96.64
3.31-3.790.26351680.22256455X-RAY DIFFRACTION97.37
3.79-4.770.21731690.1916466X-RAY DIFFRACTION98.02
4.77-35.650.24111590.20996508X-RAY DIFFRACTION98.42

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