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Yorodumi- PDB-2e8b: Crystal structure of the putative protein (Aq1419) from Aquifex a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8b | ||||||
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Title | Crystal structure of the putative protein (Aq1419) from Aquifex aeolicus VF5 | ||||||
Components | Probable molybdopterin-guanine dinucleotide biosynthesis protein A | ||||||
Keywords | BIOSYNTHETIC PROTEIN / putative protein / Aq_1419 / molybdenum cofactor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information molybdenum cofactor guanylyltransferase / molybdenum cofactor guanylyltransferase activity / Mo-molybdopterin cofactor biosynthetic process / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.61 Å | ||||||
Authors | Kumarevel, T.S. / Malathy sony, S.M. / Ponnuswamy, M.N. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the putative protein (Aq1419) from Aquifex aeolicus VF5 Authors: Kumarevel, T.S. / Malathy Sony, S.M. / Ponnuswamy, M.N. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e8b.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8b.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e8b_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 2e8b_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 2e8b_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 2e8b_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8b ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8b | 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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-Components
#1: Protein | Mass: 23389.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: mobA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codonplus-RIL-X / References: UniProt: O67413 |
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#2: 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: 1.95 Å3/Da / Density % sol: 36.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2M Ammonium Iodide, 20% PEG3350, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97891, 0.97944, 0.9 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2006 | ||||||||||||
Radiation | Monochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.61→42.1 Å / Num. all: 24264 / Num. obs: 24264 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.82 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.058 | ||||||||||||
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.341 / Num. unique all: 2403 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.61→39.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 925066.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.6359 Å2 / ksol: 0.346911 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.61→39.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.71 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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