+Open data
-Basic information
Entry | Database: PDB / ID: 2ox5 | ||||||
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Title | The SoxYZ complex of Paracoccus pantotrophus | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / IMMUNOGLOBULIN-LIKE BETA-SANDWICH FOLD | ||||||
Function / homology | Function and homology information Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Immunoglobulin E-set / Immunoglobulins ...Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å | ||||||
Authors | Bruno, S. / Sauve, V. / Berks, B.C. / Hemmings, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The SoxYZ Complex Carries Sulfur Cycle Intermediates on a Peptide Swinging Arm. Authors: Sauve, V. / Bruno, S. / Berks, B.C. / Hemmings, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ox5.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ox5.ent.gz | 154.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ox5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ox5_validation.pdf.gz | 521.1 KB | Display | wwPDB validaton report |
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Full document | 2ox5_full_validation.pdf.gz | 535.2 KB | Display | |
Data in XML | 2ox5_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 2ox5_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2ox5 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2ox5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a SoxYZ heterodimer. The crystallographic asymmetric unit contains two copies of this biological assembly. |
-Components
-Protein , 2 types, 8 molecules ZACEYBDF
#1: Protein | Mass: 11781.041 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: LMD82.5T / Gene: soxZ / Plasmid: pVS005 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9LCU8 #2: Protein | Mass: 11436.581 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: LMD82.5T / Gene: soxY / Plasmid: pVS005 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9LCU9 |
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-Non-polymers , 4 types, 907 molecules
#3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8.0, 5 mM beta-mercaptoethanol and 200 mM NaCl mixed with 2 microl of 28-30 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM ...Details: 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8.0, 5 mM beta-mercaptoethanol and 200 mM NaCl mixed with 2 microl of 28-30 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793, 0.8731 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.981→102.147 Å / Num. all: 59443 / Num. obs: 59443 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 8.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.416 / SU ML: 0.099 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.153 / 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: 22.604 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.032 Å / Total num. of bins used: 20
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