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- PDB-2fhd: Crystal structure of Crb2 tandem tudor domains -

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Basic information

Entry
Database: PDB / ID: 2fhd
TitleCrystal structure of Crb2 tandem tudor domains
ComponentsDNA repair protein rhp9/CRB2
KeywordsCELL CYCLE / Tamdem Tudor Domains
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
SH3 type barrels. - #810 / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / SH3 type barrels. - #140 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...SH3 type barrels. - #810 / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / SH3 type barrels. - #140 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / DNA repair protein crb2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLee, J. / Botuyan, M.V. / Thompson, J.R. / Mer, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.
Authors: Botuyan, M.V. / Lee, J. / Ward, I.M. / Kim, J.E. / Thompson, J.R. / Chen, J. / Mer, G.
History
DepositionDec 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
C: DNA repair protein rhp9/CRB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,76613
Polymers52,8173
Non-polymers95010
Water2,810156
1
C: DNA repair protein rhp9/CRB2
hetero molecules

C: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53326
Polymers105,6336
Non-polymers1,89920
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
crystal symmetry operation6_664-x+1,-x+y+1,-z-1/31
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10330 Å2
ΔGint-150 kcal/mol
Surface area43430 Å2
MethodPISA
2
C: DNA repair protein rhp9/CRB2
hetero molecules

C: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53326
Polymers105,6336
Non-polymers1,89920
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_664-x+y+1,-x+1,z-2/31
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9860 Å2
ΔGint-158 kcal/mol
Surface area43910 Å2
MethodPISA
3
A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
C: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
C: DNA repair protein rhp9/CRB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53326
Polymers105,6336
Non-polymers1,89920
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11320 Å2
ΔGint-156 kcal/mol
Surface area42450 Å2
MethodPISA
4
A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
C: DNA repair protein rhp9/CRB2
hetero molecules

A: DNA repair protein rhp9/CRB2
B: DNA repair protein rhp9/CRB2
C: DNA repair protein rhp9/CRB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53326
Polymers105,6336
Non-polymers1,89920
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9320 Å2
ΔGint-158 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.924, 116.924, 87.015
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA repair protein rhp9/CRB2 / RAD9 homolog


Mass: 17605.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: rhp9, crb2 / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA / References: GenBank: 1449177, UniProt: P87074*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 0.8M NaH2PO4, 0.8M KH2PO4, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 8, 2005 / Details: OSMIC VARIMAX
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25798 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 35.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 3.11 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.701 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1393 5.1 %RANDOM
Rwork0.192 ---
obs0.196 25798 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 60 171 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0223613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6391.9644896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.175440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49322.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.16415641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2271525
X-RAY DIFFRACTIONr_chiral_restr0.2460.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022629
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.21592
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.22418
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4260.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5011.52238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50223592
X-RAY DIFFRACTIONr_scbond_it4.13431517
X-RAY DIFFRACTIONr_scangle_it5.954.51304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 101 -
Rwork0.214 1859 -
obs--100 %

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