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- PDB-8u0g: Full-length dimer of DNA-Damage Response Protein C from Deinococc... -

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Basic information

Entry
Database: PDB / ID: 8u0g
TitleFull-length dimer of DNA-Damage Response Protein C from Deinococcus radiodurans - Crystal form xMJ7124
ComponentsDNA damage response protein C
KeywordsDNA BINDING PROTEIN / DNA Repair / Radioresistance
Function / homologycellular response to desiccation / nucleoid / cellular response to gamma radiation / DNA repair / DNA damage response / cytoplasm / DNA damage response protein C
Function and homology information
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.28 Å
AuthorsSzabla, R. / Li, M.C. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2008R00075 Canada
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism.
Authors: Szabla, R. / Li, M. / Warner, V. / Song, Y. / Junop, M.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage response protein C
B: DNA damage response protein C


Theoretical massNumber of molelcules
Total (without water)50,4832
Polymers50,4832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-50 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.039, 111.039, 101.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein DNA damage response protein C


Mass: 25241.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Strain: R1 / Gene: ddrC / Plasmid: pMJ5741
Details (production host): WT DdrC with N-term His-tag and TEV site in pDEST-527 backbone
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): (DE3)-T1R / References: UniProt: Q9RYE6

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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: 3.48 Å3/Da / Density % sol: 64.6 %
Description: Hexagonal bipyramid ~100um in width, depth and height
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 ul of protein solution was mixed with 1.5 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution Protein solution: 140uM DdrC, 200mM ...Details: 1.5 ul of protein solution was mixed with 1.5 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution Protein solution: 140uM DdrC, 200mM Sodium sulfate, 1mM Magnesium chloride, 20mM Sodium citrate / Citric acid, pH 6.5 Crystallization solution (Wizard Classics 1 #22) 10% (v/v) 2-propanol 100mM Tris-base/HCl, pH 8.5 Well solution: 1.5M Ammonium sulfate
PH range: 6.0 - 8.5 / Temp details: Temperature-controlled incubator at 20C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 4.277→96.163 Å / Num. obs: 5236 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 170.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.064 / Net I/σ(I): 9.9
Reflection shellResolution: 4.277→4.351 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 242 / CC1/2: 0.889 / Rpim(I) all: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudio2.4.0data collection
autoPROC1.0.5data processing
XDS20220220data reduction
pointless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.28→69.81 Å / SU ML: 0.4185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3457 243 4.67 %
Rwork0.2524 4965 -
obs0.2567 5208 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 215.44 Å2
Refinement stepCycle: LAST / Resolution: 4.28→69.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 0 0 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643476
X-RAY DIFFRACTIONf_angle_d0.97764710
X-RAY DIFFRACTIONf_chiral_restr0.0507527
X-RAY DIFFRACTIONf_plane_restr0.0079631
X-RAY DIFFRACTIONf_dihedral_angle_d11.38621299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.28-5.390.41961230.33222424X-RAY DIFFRACTION99.53
5.39-69.810.31541200.22422541X-RAY DIFFRACTION99.37

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