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- PDB-3uv0: Crystal structure of the drosophila MU2 FHA domain -

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Basic information

Entry
Database: PDB / ID: 3uv0
TitleCrystal structure of the drosophila MU2 FHA domain
ComponentsMutator 2, isoform B
KeywordsPROTEIN BINDING / FHA / dimerization
Function / homology
Function and homology information


regulation of pericentric heterochromatin formation / regulation of chromatin organization / chromosome, centromeric region / euchromatin / double-strand break repair / transcription coactivator activity / nucleus
Similarity search - Function
Mutator 2, fork head associated domain / Mutator 2 Fork head associated domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / BRCT domain / BRCT domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
PAX-interacting protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsLuo, S. / Ye, K.
CitationJournal: Febs Lett. / Year: 2012
Title: Dimerization, but not phosphothreonine binding, is conserved between the forkhead-associated domains of Drosophila MU2 and human MDC1
Authors: Luo, S. / Ye, K.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mutator 2, isoform B
B: Mutator 2, isoform B


Theoretical massNumber of molelcules
Total (without water)22,1262
Polymers22,1262
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.860, 99.860, 38.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Mutator 2, isoform B


Mass: 11062.803 Da / Num. of mol.: 2 / Fragment: FHA domain, UNP residues 1-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mu2, Dmel_CG1960 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9W061
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Calcium acetate, pH 7.0, 18% PEG 3350, 50mM KCl, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 20767

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→18.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.857 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 879 5.1 %RANDOM
Rwork0.1778 ---
obs0.1802 17351 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.05 Å2 / Biso mean: 18.1713 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 135 1624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221517
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9782041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44523.43864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1315279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021112
X-RAY DIFFRACTIONr_mcbond_it0.9441.5972
X-RAY DIFFRACTIONr_mcangle_it1.83821549
X-RAY DIFFRACTIONr_scbond_it3.1193545
X-RAY DIFFRACTIONr_scangle_it5.2934.5492
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 64 -
Rwork0.186 1180 -
all-1244 -
obs--98.42 %

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