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Yorodumi- PDB-2ogx: The crystal structure of the molybdenum storage protein from Azot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ogx | ||||||
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Title | The crystal structure of the molybdenum storage protein from Azotobacter vinelandii loaded with polyoxotungstates (WSto) | ||||||
Components | (Molybdenum storage protein subunit ...) x 2 | ||||||
Keywords | METAL BINDING PROTEIN / open alpha/beta structure | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Schemberg, J. / Warkentin, E. / Ermler, U. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: Towards Biological Supramolecular Chemistry: A Variety of Pocket-Templated, Individual Metal Oxide Cluster Nucleations in the Cavity of a Mo/W-Storage Protein. Authors: Schemberg, J. / Schneider, K. / Demmer, U. / Warkentin, E. / Muller, A. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ogx.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ogx.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ogx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ogx_validation.pdf.gz | 800.8 KB | Display | wwPDB validaton report |
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Full document | 2ogx_full_validation.pdf.gz | 813 KB | Display | |
Data in XML | 2ogx_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 2ogx_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2ogx ftp://data.pdbj.org/pub/pdb/validation_reports/og/2ogx | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Details | The biological assembly is a heterohexamer, (AB)3, generated from the heterodimer AB by the three fold axis: -y+1, x-y, z, and y-x+1, -x+1, z, respectively. |
-Components
-Molybdenum storage protein subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 29564.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DSMZ 366 / References: UniProt: P84308 |
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#2: Protein | Mass: 28707.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DSMZ 366 / References: UniProt: P84253 |
-Non-polymers , 6 types, 419 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | ChemComp-WO3 / | ||||
#5: Chemical | ChemComp-ATP / | ||||
#6: Chemical | ChemComp-W / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M MOPS, 0.05M sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.6→10 Å / Num. all: 107052 / Num. obs: 107052 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 6.5 / Net I/σ(I): 10.3 | ||||||||||||||||||
Reflection shell | Resolution: 0→0 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 5.15 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.905 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 25.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.603→1.644 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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