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Yorodumi- PDB-2h5y: Crystallographic structure of the Molybdate-Binding Protein of Xa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h5y | ||||||
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Title | Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate | ||||||
Components | Molybdate-binding periplasmic protein | ||||||
Keywords | METAL TRANSPORT / Molybdate-binding protein / ModA / Xanthomonas axonopodis pv. citri | ||||||
Function / homology | Function and homology information molybdate ion binding / tungstate binding / molybdate ion transport / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Balan, A. / Santacruz, C.P. / Ferreira, L.C.S. / Barbosa, J.A.R.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization, data collection and phasing of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri Authors: Santacruz, C.P. / Balan, A. / Ferreira, L.C. / 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 | 2h5y.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h5y.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 2h5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h5y_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 2h5y_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 2h5y_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 2h5y_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/2h5y ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h5y | HTTPS FTP |
-Related structure data
Related structure data | 1amfS 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: 26696.189 Da / Num. of mol.: 3 / Fragment: residues 1-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria) Species: Xanthomonas axonopodis / Strain: 306 / Gene: modA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PHA1 #2: Chemical | ChemComp-SO4 / #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: 2.05 Å3/Da / Density % sol: 40.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M Tris-HCl, 30% PEG 4000 , pH 8.5, 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: Jan 13, 2005 / 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: 1.7→50 Å / Num. all: 72786 / Num. obs: 72786 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.062 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.415 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AMF Resolution: 1.7→30.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.472 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; Although waters 481 and 659 are about 0.02 Ang outside the limit of 0.15 Ang stated in the remark 375, they are considered by the authors ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; Although waters 481 and 659 are about 0.02 Ang outside the limit of 0.15 Ang stated in the remark 375, they are considered by the authors to be in special positions.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.879 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.697→1.741 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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