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- PDB-3umz: Crystal Structure of the human MDC1 FHA Domain -

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Basic information

Entry
Database: PDB / ID: 3umz
TitleCrystal Structure of the human MDC1 FHA Domain
ComponentsMediator of DNA damage checkpoint protein 1
KeywordsPROTEIN BINDING / FHA / Phosphothreonine binding
Function / homology
Function and homology information


chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / nuclear body / DNA repair / focal adhesion / DNA damage response / nucleoplasm / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain profile. ...Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsLuo, S. / Ye, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain
Authors: Liu, J. / Luo, S. / Zhao, H. / Liao, J. / Li, J. / Yang, C. / Xu, B. / Stern, D.F. / Xu, X. / Ye, K.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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

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Assembly

Deposited unit
A: Mediator of DNA damage checkpoint protein 1
B: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)25,0192
Polymers25,0192
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.987, 58.856, 67.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mediator of DNA damage checkpoint protein 1 / Nuclear factor with BRCT domains 1


Mass: 12509.480 Da / Num. of mol.: 2 / Fragment: FHA domain, residues 27-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1, KIAA0170, NFBD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14676
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.29 Å3/Da / Density % sol: 46.2 % / Mosaicity: 0.51 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.1M HEPES (pH 7.5), 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: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 28513 / % possible obs: 98.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.108 / Χ2: 1.49 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.684.80.58614003.486199.5
1.68-1.715.30.53714111.254199.6
1.71-1.745.90.49614171.208199.9
1.74-1.786.50.45314311.1031100
1.78-1.8270.44714191.6481100
1.82-1.867.10.41414091.3851100
1.86-1.97.20.38814241.041100
1.9-1.967.10.3814202.113199.9
1.96-2.017.20.2314241.1071100
2.01-2.087.10.214331.1941100
2.08-2.157.10.16714160.9961100
2.15-2.247.10.14414491.1911100
2.24-2.3470.13214421.286199.9
2.34-2.467.10.10814381.1071100
2.46-2.6270.09914331.2641100
2.62-2.826.70.09214531.5471100
2.82-3.116.40.07814551.937199.9
3.11-3.556.10.06114692.13199.9
3.55-4.485.60.04514702.049197.9
4.48-504.70.03913001.776182.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→19.74 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.052 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1415 5.1 %RANDOM
Rwork0.2347 ---
obs0.2364 27817 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.7 Å2 / Biso mean: 20.2059 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 170 1814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221688
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9862290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09222.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86915286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8781514
X-RAY DIFFRACTIONr_chiral_restr0.090.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221282
X-RAY DIFFRACTIONr_mcbond_it0.8151.51052
X-RAY DIFFRACTIONr_mcangle_it1.64521702
X-RAY DIFFRACTIONr_scbond_it2.4093636
X-RAY DIFFRACTIONr_scangle_it3.8774.5588
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 108 -
Rwork0.246 1906 -
all-2014 -
obs--98.73 %

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