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Yorodumi- PDB-2ohd: Crystal structure of hypothetical molybdenum cofactor biosynthesi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ohd | ||||||
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Title | Crystal structure of hypothetical molybdenum cofactor biosynthesis protein C from Sulfolobus tokodaii | ||||||
Components | Probable molybdenum cofactor biosynthesis protein C | ||||||
Keywords | BIOSYNTHETIC PROTEIN / alpha + beta | ||||||
Function / homology | Function and homology information cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii str. 7 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yoshida, H. / Yamada, M. / Kuramitsu, S. / Kamitori, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure of a putative molybdenum-cofactor biosynthesis protein C (MoaC) from Sulfolobus tokodaii (ST0472) Authors: Yoshida, H. / Yamada, M. / Kuramitsu, S. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ohd.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ohd.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ohd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ohd_validation.pdf.gz | 476.5 KB | Display | wwPDB validaton report |
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Full document | 2ohd_full_validation.pdf.gz | 497.9 KB | Display | |
Data in XML | 2ohd_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 2ohd_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/2ohd ftp://data.pdbj.org/pub/pdb/validation_reports/oh/2ohd | HTTPS FTP |
-Related structure data
Related structure data | 1ekrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17152.123 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Gene: ST0472 / Production host: Escherichia coli (E. coli) / References: UniProt: Q975D5 #2: 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: 2.34 Å3/Da / Density % sol: 47.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 3000, 0.1M HEPES, 0.2M magnesium chloride , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 48362 / Num. obs: 48362 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.268 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EKR Resolution: 2.2→45.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 52270.57 / 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: 49.5666 Å2 / ksol: 0.373335 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→45.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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