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Yorodumi- PDB-3kbq: The crystal structure of the protein CinA with unknown function f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbq | ||||||
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Title | The crystal structure of the protein CinA with unknown function from Thermoplasma acidophilum | ||||||
Components | Protein Ta0487 | ||||||
Keywords | structural genomics / unknown function / CinA / Protein Structure Initiative / MCSG / PSI-2 / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Putative competence-damage inducible protein, Archaea / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Zhang, R. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein CinA with unknown function from Thermoplasma acidophilum Authors: Zhang, R. / Li, H. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbq.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbq.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kbq_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 3kbq_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 3kbq_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3kbq_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbq ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbq | HTTPS FTP |
-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 | This protein exists as dimer. The deposited MolA/MolB represent the dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 18552.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: GI:10639657, Ta0487 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HKV6 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40% PEG600, 0.1M citrate, pH 5.5, 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: 0.9794, 0.9796 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2009 / Details: mirrors | |||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→55.99 Å / Num. all: 21287 / Num. obs: 20972 / % possible obs: 98.52 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 23.5 | |||||||||
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1607 / % possible all: 97.64 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→55.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.649 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.173 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 31.506 Å2
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Refinement step | Cycle: LAST / Resolution: 2→55.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 115.197 Å / Origin y: -3.298 Å / Origin z: 44.249 Å
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Refinement TLS group |
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