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Yorodumi- PDB-2g2c: Putative molybdenum cofactor biosynthesis protein from Corynebact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2c | ||||||
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Title | Putative molybdenum cofactor biosynthesis protein from Corynebacterium diphtheriae. | ||||||
Components | Putative molybdenum cofactor biosynthesis protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative molybdenum cofactor biosynthesis protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | 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 / Putative molybdenum cofactor biosynthesis protein Function and homology information | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Osipiuk, J. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of putative molybdenum cofactor biosynthesis protein from Corynebacterium diphtheriae. Authors: Osipiuk, J. / Li, H. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2c.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2c.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2c_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 2g2c_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 2g2c_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2g2c_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2c ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2c | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17814.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP0503 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6NJA6 |
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#2: Chemical | ChemComp-NA / |
#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: 2.13 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes buffer, 3 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97894 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 9, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→32.51 Å / Num. all: 23460 / Num. obs: 23460 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 49.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.23 / Num. unique all: 773 / % possible all: 49.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→32.52 Å / Cor.coef. Fo:Fc: 0.965 / SU B: 2.149 / SU ML: 0.037 / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: 18.631 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→32.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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