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- PDB-2etx: Crystal Structure of MDC1 Tandem BRCT Domains -

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Basic information

Entry
Database: PDB / ID: 2etx
TitleCrystal Structure of MDC1 Tandem BRCT Domains
ComponentsMediator of DNA damage checkpoint protein 1
KeywordsCELL CYCLE / TANDEM BRCT DOMAINS HISTONE GAMMA-H2AX
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 / site of double-strand break / chromosome / Processing of DNA double-strand break ends / nuclear body / focal adhesion / DNA repair / DNA damage response / nucleoplasm / nucleus
Similarity search - Function
: / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / 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 / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.33 Å
AuthorsWasielewski, E. / Kim, Y. / Joachimiak, A. / Thompson, J.R. / Mer, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Basis for the Association of Microcephalin (MCPH1) Protein with the Cell Division Cycle Protein 27 (Cdc27) Subunit of the Anaphase-promoting Complex.
Authors: Singh, N. / Wiltshire, T.D. / Thompson, J.R. / Mer, G. / Couch, F.J.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Database references
Revision 1.4Feb 22, 2012Group: Database references
Revision 1.5Feb 14, 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)45,8272
Polymers45,8272
Non-polymers00
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.890, 44.350, 63.100
Angle α, β, γ (deg.)70.98, 86.45, 61.91
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22913.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDC1 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA (DE3) / References: UniProt: Q14676
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES 0.1M, PEG 8000 15%, ETHYLENE GLYCOL 15%, AMMONIUM ACETATE 0.2M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954, 0.97967, 0.98120
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.979671
30.98121
ReflectionResolution: 1.33→36.84 Å / Num. all: 85639 / Num. obs: 85639
Reflection shellResolution: 1.33→1.364 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.33→59.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 0.826 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22574 4300 5 %RANDOM
Rwork0.20158 ---
all0.201 85639 --
obs0.20279 81339 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20.08 Å20.16 Å2
2---0.15 Å2-0.5 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.33→59.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 0 441 3440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223095
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2962.0064212
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9922.419124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9391529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21507
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22121
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8251.52003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32523180
X-RAY DIFFRACTIONr_scbond_it1.88431200
X-RAY DIFFRACTIONr_scangle_it2.7574.51031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 309 -
Rwork0.248 6012 -
obs--99.17 %

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