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Yorodumi- PDB-2omd: Crystal structure of molybdopterin converting factor subunit 2 (a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2omd | ||||||
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Title | Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5 | ||||||
Components | Molybdopterin-converting factor subunit 2 | ||||||
Keywords | LYASE / MOAE / coenzyme biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5 Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2omd.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2omd.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 2omd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/2omd ftp://data.pdbj.org/pub/pdb/validation_reports/om/2omd | 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17606.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)-RIL / References: UniProt: O67928 |
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-Non-polymers , 6 types, 387 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | #7: 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: 3.71 Å3/Da / Density % sol: 66.86 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 10% 1,2-propanediol, 25% Glycerol, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.9000, 0.9794 | ||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 15, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR | ||||||||||||
Radiation | Monochromator: SI 1 1 1 Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 36659 / % possible obs: 100 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.073 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.249 / Num. unique all: 3583 / Rsym value: 0.264 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→38.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1319976.37 / 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: 59.8037 Å2 / ksol: 0.339765 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→38.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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