+Open data
-Basic information
Entry | Database: PDB / ID: 3m03 | ||||||
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Title | Crystal structure of human Orc6 fragment | ||||||
Components | Origin recognition complex subunit 6 | ||||||
Keywords | DNA BINDING PROTEIN / helix turn helix / Origin recognition complex / DNA replication | ||||||
Function / homology | Function and homology information CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center / Orc1 removal from chromatin / DNA binding / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.5 Å | ||||||
Authors | Liu, S.X. / Wu, L.J. / Sun, J. / Wang, H.F. / Liu, Y.F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB Authors: Liu, S.X. / Balasov, M. / Wang, H.F. / Wu, L.J. / Chesnokov, I.N. / Liu, Y.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m03.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m03.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m03_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 3m03_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 3m03_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3m03_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/3m03 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m03 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10487.373 Da / Num. of mol.: 3 / Fragment: Middle Domain, reisdues 93-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORC6 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5N6 #2: Chemical | ChemComp-MES / | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES, Li2SO4, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 12005 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1226 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU B: 20.211 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.183 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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