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Yorodumi- PDB-3bjo: Crystal structure of the C-terminal domain of a possible ATP-bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjo | ||||||
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Title | Crystal structure of the C-terminal domain of a possible ATP-binding protein from Methanocaldococcus jannaschii DSM 2661 | ||||||
Components | Uncharacterized ATP-binding protein MJ1010 | ||||||
Keywords | NUCLEOTIDE BINDING PROTEIN / APC87992.1 / Methanocaldococcus jannaschii DSM 2661 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Tan, K. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of the C-terminal domain of a possible ATP-binding protein from Methanocaldococcus jannaschii DSM 2661. Authors: Tan, K. / Hatzos, C. / Moy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjo.cif.gz | 31.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjo.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjo ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Authors state that the biological unit of this polypeptide is experimentally unknown. |
-Components
#1: Protein | Mass: 12172.328 Da / Num. of mol.: 1 / Fragment: C-terminal domain: Residues 278-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Species: Methanocaldococcus jannaschii / Strain: DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 / Gene: MJ1010 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q58416 |
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#2: Chemical | ChemComp-FMT / |
#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: 3.36 Å3/Da / Density % sol: 63.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.4M Magnesium formate, 0.1M Sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→34.71 Å / Num. all: 10377 / Num. obs: 10377 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.2 / Num. unique all: 632 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→34.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.962 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.163 / ESU R Free: 0.138 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.561 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.562 Å / Origin y: -13.894 Å / Origin z: -18.814 Å
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