+Open data
-Basic information
Entry | Database: PDB / ID: 1j58 | ||||||
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Title | Crystal Structure of Oxalate Decarboxylase | ||||||
Components | YVRK PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / CUPIN / DECARBOXYKLASE / OXALATE / MANGANESE / FORMATE | ||||||
Function / homology | Function and homology information oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Anand, R. / Dorrestein, P.C. / Kinsland, C. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution. Authors: Anand, R. / Dorrestein, P.C. / Kinsland, C. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j58.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j58.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j58 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j58 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a hexamer constructed by doing a three fold and a two fold symmetry operation on chain A |
-Components
#1: Protein | Mass: 44042.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET16b / Production host: Bacteria (eubacteria) / References: UniProt: O34714 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-FMT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.95 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: PEG 4000, Tris-Hcl, sodium chloride, pH 8.0, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: .9791, 0.9794, 0.9641, 0.9807 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→29.83 Å / Num. all: 57048 / Num. obs: 57048 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / % possible all: 99.7 | |||||||||||||||
Reflection | *PLUS Num. obs: 57307 / % possible obs: 99.9 % / Redundancy: 7.1 % / Num. measured all: 406760 / Rmerge(I) obs: 0.083 | |||||||||||||||
Reflection shell | *PLUS Lowest resolution: 1.84 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 1.75→29.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3802941.91 / Data cutoff high rms absF: 3802941.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.7172 Å2 / ksol: 0.387726 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection obs: 57039 / % reflection Rfree: 10 % / Rfactor all: 0.192 / Rfactor obs: 0.181 / Rfactor Rfree: 0.1784 / Rfactor Rwork: 0.1831 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.241 / Rfactor Rwork: 0.228 |