+Open data
-Basic information
Entry | Database: PDB / ID: 2oxh | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | 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 | 2oxh.cif.gz | 322.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oxh.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxh ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxh | HTTPS FTP |
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-Related structure data
Related structure data | 2ox5SC 2oxgC 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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2 |
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3 |
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4 |
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Unit cell |
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Details | THE BIOLOGICAL UNIT IS A SOXYZ HETERODIMER. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS 4 COPIES OF THE BIOLOGICAL UNIT. |
-Components
#1: Protein | Mass: 11663.068 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LCU8 #2: Protein | Mass: 12469.990 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LCU9 #3: Chemical | ChemComp-EDO / #4: 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: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1 microL of 10 mg ml-1 protein in 10 mM Tris pH 8.0 with 1 microL of 100 mM Na-acetate pH 4.75, 200 mM (NH4)2SO4, 31 % (w/v) PEG 3350, 2% (w/v) glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2005 / Details: Double Si(111) monoichromation |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→101.687 Å / Num. all: 34657 / Num. obs: 34657 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.144 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OX5 Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 Isotropic thermal model: ISOTROPIC INDIVIDUAL PLUS TLSMD GROUP REFINEMENT Cross valid method: THROUGHOUT / ESU R Free: 0.269 / 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: 14.633 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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