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Yorodumi- PDB-2z4s: Crystal structure of domain III from the Thermotoga maritima repl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z4s | ||||||
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Title | Crystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA | ||||||
Components | Chromosomal replication initiator protein dnaA | ||||||
Keywords | DNA BINDING PROTEIN / AAA+ ATPase / domain III (ATPase domain) / ATP-binding / Cytoplasm / DNA replication / DNA-binding / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of DNA replication / DNA replication origin binding / DNA replication initiation / DNA replication / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Fujikawa, N. / Ozaki, S. / Kagawa, W. / Park, S.-Y. / Katayama, T. / Kurumizaka, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: A Common Mechanism for the ATP-DnaA-dependent Formation of Open Complexes at the Replication Origin. Authors: Ozaki, S. / Kawakami, H. / Nakamura, K. / Fujikawa, N. / Kagawa, W. / Park, S.-Y. / Yokoyama, S. / Kurumizaka, H. / Katayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z4s.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z4s.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2z4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z4s_validation.pdf.gz | 813.9 KB | Display | wwPDB validaton report |
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Full document | 2z4s_full_validation.pdf.gz | 831.4 KB | Display | |
Data in XML | 2z4s_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2z4s_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/2z4s ftp://data.pdbj.org/pub/pdb/validation_reports/z4/2z4s | HTTPS FTP |
-Related structure data
Related structure data | 2z4rC 1l8qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 50381.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: dnaA / Plasmid: pBAD18 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P46798 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.6M LITHIUM SULFATE, 0.05M MAGNESIUM SULFATE, 0.05M Na-HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2004 / Details: monochromator |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 11053 / Num. obs: 10640 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / Num. unique all: 812 / % possible all: 74.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L8Q Resolution: 3→48.12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→48.12 Å
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Refine LS restraints |
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LS refinement shell |
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