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- PDB-8u1j: N-Terminal domain of DNA-Damage Response Protein C (DdrC) from De... -

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Basic information

Entry
Database: PDB / ID: 8u1j
TitleN-Terminal domain of DNA-Damage Response Protein C (DdrC) from Deinococcus radiodurans - Crystal form xMJ7102
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSzabla, R. / Song, Y. / 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
DepositionSep 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Jul 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 1.3Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage response protein C


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water00
1
A: DNA damage response protein C

A: DNA damage response protein C


Theoretical massNumber of molelcules
Total (without water)28,8002
Polymers28,8002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area1750 Å2
ΔGint-26 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.410, 73.410, 110.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein DNA damage response protein C


Mass: 14399.754 Da / Num. of mol.: 1 / Mutation: delta(99-231)
Source method: isolated from a genetically manipulated source
Details: Selenium-derivatized N-terminal domain (residues 1-98) of DdrC from D.radiodurans with an N-terminal His-tag fusion separated by a flexible linker and a TEV protease site
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 (TEV-cleavable)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): (DE3)-T1R / References: UniProt: Q9RYE6
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Square-base bipyramid <0.1mm in all dimensions
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. During crystallization, an unknown ...Details: 3.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. During crystallization, an unknown protease contaminant in the protein solution cleaved FL DdrC between residues 98 and 99, allowing for crystallization of residues 1-98. Protein solution: 257uM DdrC, 800mM NaCl 20mM Tris, pH 8.0 5% (v/v) Glycerol Unknown protease contaminant Crystallization solution (Midas1 - MD1-59 condition #91): 15% (v/v) Sokolan-CP42 200mM Potassium citrate tribasic Well solution: 3.25M Ammonium sulfate
Temp details: Termperature-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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97995 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2019 / Details: CMCF-ID optics setup
RadiationMonochromator: double crystal multilayer monochromator (DCMM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97995 Å / Relative weight: 1
ReflectionResolution: 2.972→37.79 Å / Num. obs: 3335 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 84.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.014 / Rrim(I) all: 0.062 / Net I/σ(I): 33.7
Reflection shellResolution: 2.972→3.023 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 164 / CC1/2: 0.956 / Rpim(I) all: 0.107 / Rrim(I) all: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxDCdata collection
autoPROC1.0.5 (2022-11-21)data processing
XDS20190315data reduction
XSCALE20230630data scaling
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.79 Å / SU ML: 0.1611 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.7981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2573 155 4.79 %
Rwork0.2252 3082 -
obs0.2268 3237 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.09 Å2
Refinement stepCycle: LAST / Resolution: 3→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 0 0 748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0198765
X-RAY DIFFRACTIONf_angle_d1.66171042
X-RAY DIFFRACTIONf_chiral_restr0.0855116
X-RAY DIFFRACTIONf_plane_restr0.014139
X-RAY DIFFRACTIONf_dihedral_angle_d11.2251278
LS refinement shellResolution: 3→37.79 Å
RfactorNum. reflection% reflection
Rfree0.2573 155 -
Rwork0.2252 3082 -
obs--99.91 %

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