+Open data
-Basic information
Entry | Database: PDB / ID: 5c8h | ||||||
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Title | Crystal structure of ORC2 C-terminal domain | ||||||
Components | Origin recognition complex subunit 2 | ||||||
Keywords | REPLICATION / Structural Genomics / DNA replication / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / inner kinetochore / nuclear origin of replication recognition complex / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / heterochromatin / Activation of ATR in response to replication stress ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / inner kinetochore / nuclear origin of replication recognition complex / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / heterochromatin / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / chromosome, telomeric region / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Tempel, W. / Xu, C. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of ORC2 C-terminal domain Authors: Tempel, W. / Xu, C. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c8h.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c8h.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 5c8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8h ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8h | HTTPS FTP |
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-Related structure data
Related structure data | 4xgcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The extent of the biological unit was not examined in this experiment. |
-Components
#1: Protein | Mass: 13813.487 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 458-577) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORC2, ORC2L / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q13416 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG-3350, 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792604 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792604 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.01→47.66 Å / Num. obs: 8700 / % possible obs: 99.8 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.024 / Net I/σ(I): 21.5 / Num. measured all: 96076 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polyalanine coordinates derived from PDB entry 4XGC. Resolution: 2.01→47.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2429 / WRfactor Rwork: 0.1825 / FOM work R set: 0.8216 / SU B: 9.777 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1792 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Data were reduced with HKL3000 for structure solution and early refinement. Molecular replacement was followed by simulated annealing refinement with PHENIX, subsequent phase improvement and ...Details: Data were reduced with HKL3000 for structure solution and early refinement. Molecular replacement was followed by simulated annealing refinement with PHENIX, subsequent phase improvement and automated model buidling with ARP/WARP. Diffraction data were reduced with XDS/AIMLESS for later refinement steps.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.98 Å2 / Biso mean: 39.091 Å2 / Biso min: 26.46 Å2
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Refinement step | Cycle: final / Resolution: 2.01→47.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.012→2.064 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.851 Å / Origin y: 13.1035 Å / Origin z: -5.9789 Å
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