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- PDB-2ado: Crystal Structure Of The Brct Repeat Region From The Mediator of ... -

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Basic information

Entry
Database: PDB / ID: 2ado
TitleCrystal Structure Of The Brct Repeat Region From The Mediator of DNA damage checkpoint protein 1, MDC1
ComponentsMediator of DNA damage checkpoint protein 1
KeywordsCELL CYCLE / BRCT repeats
Function / homology
Function and homology information


protein localization to site of double-strand break / DNA replication checkpoint signaling / 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 ...protein localization to site of double-strand break / DNA replication checkpoint signaling / 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. / BRCT domain ...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: 1.45 Å
AuthorsLee, M.S. / Edwards, R.A. / Thede, G.L. / Glover, J.N.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of the BRCT Repeat Domain of MDC1 and Its Specificity for the Free COOH-terminal End of the {gamma}-H2AX Histone Tail.
Authors: Lee, M.S. / Edwards, R.A. / Thede, G.L. / Glover, J.N.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,0202
Polymers43,0202
Non-polymers00
Water4,612256
1
A: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)21,5101
Polymers21,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mediator of DNA damage checkpoint protein 1


Theoretical massNumber of molelcules
Total (without water)21,5101
Polymers21,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.051, 44.440, 61.942
Angle α, β, γ (deg.)72.95, 87.54, 61.80
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: 21509.957 Da / Num. of mol.: 2 / Fragment: Residues 1891-2086
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): Gold99 / References: UniProt: Q14676
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.244.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop8PEG 8000, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2982vapor diffusion, hanging drop4.2Sodium dihydrogen orthophosphate, Potassium phosphate dibasic, Sodium citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159,0.9795471,1.019876
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2004
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
20.97954711
31.0198761
Reflection

D res high: 2.7 Å / D res low: 100 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2% possible obs
3.11406990.1080.85895.5
6.52202080.1130.91798.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.8210094.510.0530.9333.2
4.625.8296.910.0580.8393.2
4.034.6297.210.0610.8683.2
3.664.039710.0850.9033.2
3.43.669710.110.9013.1
3.23.496.710.160.8763.2
3.043.296.610.240.8443.2
2.913.0496.610.3110.8343.2
2.82.9196.110.4110.7953.1
2.72.886.210.5220.7612.8
5.8210099.120.0620.9586.4
4.625.8299.520.0610.956.6
4.034.6299.320.0610.9456.6
3.664.039920.0840.9426.6
3.43.6698.820.1010.9516.6
3.23.498.720.140.9416.7
3.043.298.620.2060.9146.6
2.913.0498.520.2740.8696.7
2.82.9198.320.3320.8466.6
2.72.894.120.4460.8375.7
ReflectionResolution: 1.45→30 Å / Num. all: 116808 / Num. obs: 60634 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 / Χ2: 1.021
Reflection shellResolution: 1.45→1.5 Å / % possible obs: 75.9 % / Rmerge(I) obs: 0.38 / Num. measured obs: 5061 / Χ2: 0.824 / % possible all: 75.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 2.7 Å / D res low: 100 Å / FOM : 0.35 / Reflection: 19939
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.979512.76-8.13
12 wavelength21.01994.52-2.84
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.140.9930.9940.9970.705
2Se16.4130.0180.1090.3420.613
3Se600.4970.9960.4960.804
4Se600.5250.0920.8450.837
5Se40.8280.3980.9540.0080.806
6Se600.9050.9540.5130.928
7Se51.190.3030.1450.641.266
8Se45.4440.0750.0620.240.675
Phasing MAD shell
Resolution (Å)FOM Reflection
9.83-1000.57891
6.17-9.830.531647
4.81-6.170.512093
4.07-4.810.462516
3.6-4.070.42810
3.25-3.60.33109
2.99-3.250.223382
2.79-2.990.163491
Phasing dmFOM : 0.65 / FOM acentric: 0.65 / FOM centric: 0 / Reflection: 19940 / Reflection acentric: 19940 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.7-29.5580.770.77859859
4.8-7.70.760.7626812681
3.9-4.80.790.7933703370
3.4-3.90.760.7634333433
2.9-3.40.570.5760096009
2.7-2.90.410.4135883588

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.45→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2991 4.5 %RANDOM
Rwork0.195 ---
all-60634 --
obs-60499 90.9 %-
Solvent computationBsol: 47.048 Å2
Displacement parametersBiso mean: 12.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.669 Å20.131 Å2-0.444 Å2
2--0.796 Å20.876 Å2
3----1.465 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 0 256 3255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 1.45→1.5 Å /
Num. reflection% reflection
obs5061 75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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