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- PDB-4s3h: Crystal structure of S. pombe Mdb1 FHA domain -

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Basic information

Entry
Database: PDB / ID: 4s3h
TitleCrystal structure of S. pombe Mdb1 FHA domain
ComponentsMdb1
KeywordsUNKNOWN FUNCTION / Mdb1 / forkhead-associated domain (FHA domain) / dimerization
Function / homology
Function and homology information


mitotic spindle midzone / mitotic G2 DNA damage checkpoint signaling / site of double-strand break / nucleus / cytoplasm
Similarity search - Function
: / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
DNA damage response protein Mdb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.701 Å
AuthorsLuo, S. / Ye, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Dimerization Mediated by a Divergent Forkhead-associated Domain Is Essential for the DNA Damage and Spindle Functions of Fission Yeast Mdb1.
Authors: Luo, S. / Xin, X. / Du, L.L. / Ye, K. / Wei, Y.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mdb1
B: Mdb1
C: Mdb1
D: Mdb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5817
Polymers57,2924
Non-polymers2883
Water36020
1
A: Mdb1
B: Mdb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9345
Polymers28,6462
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-49 kcal/mol
Surface area9860 Å2
MethodPISA
2
C: Mdb1
D: Mdb1


Theoretical massNumber of molelcules
Total (without water)28,6462
Polymers28,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.073, 91.073, 224.503
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Mdb1


Mass: 14323.102 Da / Num. of mol.: 4 / Fragment: FHA domain, UNP residues 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14079
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium acetate, pH 5.2, 1.8 M ammonium sulfate, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 15871 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.102 / Χ2: 0.947 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.89.90.67315240.854199.8
2.8-2.919.80.55315380.875199.8
2.91-3.049.80.40715590.913199.8
3.04-3.29.80.32815370.9581100
3.2-3.49.70.19115700.9531100
3.4-3.669.70.11515690.9631100
3.66-4.039.60.08115731.019199.9
4.03-4.69.50.05716000.9851100
4.6-5.779.30.05216410.9941100
5.77-208.60.0417600.957199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.701→19.759 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 804 5.08 %
Rwork0.2185 --
obs0.2211 15820 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.38 Å2 / Biso mean: 51.9339 Å2 / Biso min: 22.42 Å2
Refinement stepCycle: LAST / Resolution: 2.701→19.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 15 20 2918

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