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- PDB-2vxb: Structure of the Crb2-BRCT2 domain -

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Basic information

Entry
Database: PDB / ID: 2vxb
TitleStructure of the Crb2-BRCT2 domain
ComponentsDNA REPAIR PROTEIN RHP9
KeywordsCELL CYCLE / BRCT / NUCLEUS / DNA DAMAGE / DNA REPLICATION INHIBITOR / PHOSPHOPROTEIN / CHECKPOINT SIGNALLING
Function / homology
Function and homology information


SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / methylated histone binding / DNA damage checkpoint signaling ...SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / methylated histone binding / DNA damage checkpoint signaling / site of double-strand break / histone binding / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / DNA repair protein crb2
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKilkenny, M.L. / Roe, S.M. / Pearl, L.H.
CitationJournal: Genes Dev. / Year: 2008
Title: Structural and Functional Analysis of the Crb2-Brct2 Domain Reveals Distinct Roles in Checkpoint Signaling and DNA Damage Repair.
Authors: Kilkenny, M.L. / Dore, A. / Roe, S.M. / Nestoras, K. / Ho, J.C.Y. / Watts, F.Z. / Pearl, L.H.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN RHP9
B: DNA REPAIR PROTEIN RHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2205
Polymers54,7972
Non-polymers4233
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-22.7 kcal/mol
Surface area24570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)56.887, 73.733, 66.772
Angle α, β, γ (deg.)90.00, 110.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA REPAIR PROTEIN RHP9 / RAD9 HOMOLOG / CHECKPOINT PROTEIN CRB2


Mass: 27398.484 Da / Num. of mol.: 2 / Fragment: BRCT DOMAIN, RESIDUE 538-778
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Strain: SP.011 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRSETB / References: UniProt: P87074
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRB2-BRCT2 (7MG/ML IN 0.05M TRIS-HCL PH7.0, 1M NACL,5MM DTT) WAS CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 20C. PLATECLUSTERS GREW FROM 2UL PROTEIN, 2UL WELL SOLUTION (0.1M NA- ...Details: CRB2-BRCT2 (7MG/ML IN 0.05M TRIS-HCL PH7.0, 1M NACL,5MM DTT) WAS CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 20C. PLATECLUSTERS GREW FROM 2UL PROTEIN, 2UL WELL SOLUTION (0.1M NA-CACODYLATE PH6.5, 7.0% PEG8000 AND 0.2M CA-ACETATE) AND 0.5UL 0.1M PR(III) ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 29876 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→35 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2274 5 %
Rwork0.189 --
obs-22338 99.9 %
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 3 130 3599

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