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- PDB-3l40: Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains -

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Basic information

Entry
Database: PDB / ID: 3l40
TitleCrystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains
ComponentsBRCT-containing protein 1
KeywordsCELL CYCLE / Brc1 / BRCT domain / Tandem BRCT repeat / phosphoserine binding domain / DNA repair / Cell Division / Mitosis
Function / homology
Function and homology information


DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / chromosome, subtelomeric region / chromatin-protein adaptor activity / rDNA heterochromatin / chromosome, centromeric region / double-strand break repair / site of double-strand break / DNA repair / nucleolus / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold ...Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCT domain, a BRCA1 C-terminus 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
BRCT-containing protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsWilliams, R.S. / Williams, J.S. / Guenther, G. / Tainer, J.A.
CitationJournal: Embo J. / Year: 2010
Title: gammaH2A binds Brc1 to maintain genome integrity during S-phase.
Authors: Williams, J.S. / Williams, R.S. / Dovey, C.L. / Guenther, G. / Tainer, J.A. / Russell, P.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: BRCT-containing protein 1
B: BRCT-containing protein 1


Theoretical massNumber of molelcules
Total (without water)49,6512
Polymers49,6512
Non-polymers00
Water7,188399
1
A: BRCT-containing protein 1


Theoretical massNumber of molelcules
Total (without water)24,8251
Polymers24,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BRCT-containing protein 1


Theoretical massNumber of molelcules
Total (without water)24,8251
Polymers24,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.472, 83.425, 87.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BRCT-containing protein 1


Mass: 24825.396 Da / Num. of mol.: 2 / Fragment: BRCT5-BRCT6 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: brc1, SPBC582.05c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10337
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / pH: 5
Details: 20-22% w/v PEG 3350, 100 mM NaCl, 100 mM K2HPO4/KH2PO4 pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.111, 0.9796, 0.9797, 1.0087
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2006
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1111
20.97961
30.97971
41.00871
ReflectionResolution: 1.55→50 Å / Num. all: 61324 / Num. obs: 61324 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.045 / Net I/σ(I): 38.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.502 / % possible all: 67

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.539 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3109 5.1 %RANDOM
Rwork0.179 ---
obs0.181 58154 94.7 %-
all-58154 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---1.32 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 399 3767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9674676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89625.374147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98315597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9011514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21672
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22407
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2339
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9731.52215
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.75823516
X-RAY DIFFRACTIONr_scbond_it6.02431381
X-RAY DIFFRACTIONr_scangle_it5.7154.51160
X-RAY DIFFRACTIONr_rigid_bond_restr5.90133596
X-RAY DIFFRACTIONr_sphericity_free8.5583407
X-RAY DIFFRACTIONr_sphericity_bonded5.38633368
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 146 -
Rwork0.195 2861 -
obs--63.68 %

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