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Yorodumi- PDB-3gzg: Crystal structure of the Xanthomonas axonopodis pv. citri molybda... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gzg | ||||||
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Title | Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S) | ||||||
Components | Molybdate-binding periplasmic protein; permease | ||||||
Keywords | METAL BINDING PROTEIN / molybdate complex / mutant K127S | ||||||
Function / homology | Function and homology information molybdate ion binding / tungstate binding / molybdate ion transport / metal ion binding Similarity search - Function | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Santacruz-Perez, C. / Pegos, V.R. / Balan, A. / Barbosa, J.A.R.G. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S) Authors: Santacruz-Perez, C. / Pegos, V.R. / Balan, A. / Barbosa, J.A.R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gzg.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gzg.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/3gzg ftp://data.pdbj.org/pub/pdb/validation_reports/gz/3gzg | HTTPS FTP |
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-Related structure data
Related structure data | 2h5yS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26542.066 Da / Num. of mol.: 3 / Mutation: K127S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria) Strain: 306 / Gene: modA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PHA1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE RESIDUE IS LEU AND IS PROBABLY A REAL VARIANT PRESENT IN NATURE. | |
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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: 2.06 Å3/Da / Density % sol: 40.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0,1M trihydrate sodium acetate, 0,2M ammonium sulfate, 30% PEG, monometil eter 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2008 / Details: mirror |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.421 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 94892 / Num. obs: 94892 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2 / Rsym value: 0.822 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H5Y Resolution: 1.55→25.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.8 / SU ML: 0.065 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / 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: 22.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.589 Å / Total num. of bins used: 20
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