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Open data
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Basic information
Entry | Database: PDB / ID: 7wi7 | |||||||||
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Title | Crystal structure of human MCM8/9 complex | |||||||||
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![]() | DNA BINDING PROTEIN / MCM8 / MCM9 / Helicase | |||||||||
Function / homology | ![]() 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 / CDC6 association with the ORC:origin complex / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / female gamete generation ...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 / CDC6 association with the ORC:origin complex / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / female gamete generation / Unwinding of DNA / MCM complex / DNA duplex unwinding / single-stranded DNA helicase activity / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / DNA helicase activity / protein localization to chromatin / double-strand break repair via homologous recombination / Orc1 removal from chromatin / chromosome / single-stranded DNA binding / DNA helicase / protein stabilization / cell cycle / DNA damage response / chromatin binding / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, J. / Liu, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human MCM8/9 complex Authors: Li, J. / Liu, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 576.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 572.2 KB | Display | ![]() |
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Full document | ![]() | 585.5 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dp3S ![]() 7dpdS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 87820.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Protein | Mass: 76848.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris propone, pH 6.0-7.5, 0.6M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 6.6→41.5 Å / Num. obs: 4153 / % possible obs: 97.81 % / Redundancy: 13.7 % / Biso Wilson estimate: 431.51 Å2 / CC1/2: 0.99 / Rsym value: 0.061 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 6.6→6.71 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 418 / Rsym value: 0.768 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DP3, 7DPD Resolution: 6.6→41.5 Å / SU ML: 1.8622 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.0802 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 627.19 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.6→41.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.1444696396 Å / Origin y: 21.367660008 Å / Origin z: -19.5298083088 Å
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Refinement TLS group | Selection details: all |