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- PDB-6l0o: WH domain of human MCM8 -

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Basic information

Entry
Database: PDB / ID: 6l0o
TitleWH domain of human MCM8
ComponentsDNA helicase MCM8
KeywordsDNA BINDING PROTEIN / WHD / Winged helix
Function / homology
Function and homology information


MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / E2F-enabled inhibition of pre-replication complex formation ...MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / E2F-enabled inhibition of pre-replication complex formation / Unwinding of DNA / MCM complex / DNA duplex unwinding / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / protein localization to chromatin / helicase activity / double-strand break repair via homologous recombination / Orc1 removal from chromatin / single-stranded DNA binding / chromosome / DNA helicase / protein stabilization / DNA damage response / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPases associated with a variety of cellular activities ...MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.21 Å
AuthorsLiu, Y. / Li, J. / Liu, L. / Zeng, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the winged-helix domain of MCM8.
Authors: Zeng, H. / Li, J. / Xu, H. / Li, H. / Liu, Y.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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: DNA helicase MCM8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7443
Polymers9,5521
Non-polymers1922
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area4860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.062, 52.062, 50.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein DNA helicase MCM8 / Minichromosome maintenance 8


Mass: 9551.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM8, C20orf154 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UJA3, DNA helicase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0-2.2M (NH4)2SO4, 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 23189 / % possible obs: 97.3 % / Redundancy: 20.3 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.014 / Rrim(I) all: 0.065 / Rsym value: 0.075 / Net I/σ(I): 51.576
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 19.8 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 5.714 / Num. unique obs: 1100 / CC1/2: 0.932 / Rpim(I) all: 0.144 / Rrim(I) all: 0.649 / Rsym value: 0.644 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
HKL-3000data reduction
SCALEPACKdata scaling
Sir2014phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.21→33.62 Å / SU ML: 0.0688 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.136
RfactorNum. reflection% reflection
Rfree0.1465 1981 8.56 %
Rwork0.1202 --
obs0.1225 23143 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.03 Å2
Refinement stepCycle: LAST / Resolution: 1.21→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 10 82 682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075650
X-RAY DIFFRACTIONf_angle_d0.8558885
X-RAY DIFFRACTIONf_chiral_restr0.073792
X-RAY DIFFRACTIONf_plane_restr0.006118
X-RAY DIFFRACTIONf_dihedral_angle_d14.6977246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.240.15471350.13381445X-RAY DIFFRACTION93.27
1.24-1.270.13461400.12021480X-RAY DIFFRACTION95.91
1.27-1.310.13571410.11511466X-RAY DIFFRACTION95.94
1.31-1.350.14811400.1161472X-RAY DIFFRACTION96.35
1.35-1.40.14351410.11391515X-RAY DIFFRACTION96.34
1.4-1.460.13231390.10561484X-RAY DIFFRACTION97.13
1.46-1.520.12081370.09461517X-RAY DIFFRACTION97.35
1.52-1.60.12421430.09721513X-RAY DIFFRACTION97.93
1.6-1.710.13931440.09991521X-RAY DIFFRACTION98.06
1.71-1.840.12321370.10331534X-RAY DIFFRACTION98.41
1.84-2.020.13361440.1111528X-RAY DIFFRACTION98.53
2.02-2.310.12091400.10631546X-RAY DIFFRACTION99.23
2.31-2.920.13931480.12111558X-RAY DIFFRACTION99.59
2.92-33.620.17911520.14361583X-RAY DIFFRACTION99.94

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