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Yorodumi- PDB-4ndq: Crystal structure Molybdenum Storage Protein with fully Mo-loaded... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ndq | ||||||
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Title | Crystal structure Molybdenum Storage Protein with fully Mo-loaded cavity | ||||||
Components | (Molybdenum storage protein subunit ...) x 2 | ||||||
Keywords | METAL BINDING PROTEIN / Rossmann Fold / Molybdenum Storage / ATP Binding / Molybdenum Binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / start from known model / Resolution: 1.751 Å | ||||||
Authors | Poppe, J. / Warkentin, E. / Demmer, U. / Ermler, U. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2014 Title: Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein. Authors: Poppe, J. / Warkentin, E. / Demmer, U. / Kowalewski, B. / Dierks, T. / Schneider, K. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ndq.cif.gz | 219.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ndq.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ndq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ndq_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 4ndq_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 4ndq_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 4ndq_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/4ndq ftp://data.pdbj.org/pub/pdb/validation_reports/nd/4ndq | HTTPS FTP |
-Related structure data
Related structure data | 4ndoC 4ndpC 4ndrC 4f6tS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Details | Asymetric unit contains a dimer of subunit A and B; the biological unit is a hexamer generated from the dimer by the operations (1)x,y,z (2)-y,x-y,z (3)-x+y,-x,z (4)-x,-y,z+1/2 (5)y,-x+y,z+1/2 (6)x-y,x,z+1/2 (7)x,y,-z (8)x-y,-y,-z (9)-x,-x+y,-z (10)-y,-x,-z+1/2 (11)-x+y,y,-z+1/2 (12)x,x-y,-z+1/2 |
-Components
-Molybdenum storage protein subunit ... , 2 types, 2 molecules BA
#1: Protein | Mass: 28378.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: ATCC 13705 / References: UniProt: P84253 |
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#2: Protein | Mass: 29376.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATCC 13705 / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: ATCC 13705 / References: UniProt: P84308 |
-Non-polymers , 6 types, 331 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MO / #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-M10 / ( | #8: 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: 3.89 Å3/Da / Density % sol: 68.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0,1 M NaCitrate, 1.1 M (NH4)HCitrate, 0.1 M (NH4)H2PO4, 15% (v/v)EG, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 91252 / Num. obs: 91252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.75→1.85 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: start from known model Starting model: 4F6T Resolution: 1.751→9.997 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 21.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.751→9.997 Å
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Refine LS restraints |
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LS refinement shell |
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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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