+Open data
-Basic information
Entry | Database: PDB / ID: 1tlb | ||||||
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Title | Yeast coproporphyrinogen oxidase | ||||||
Components | Coproporphyrinogen III oxidase | ||||||
Keywords | OXIDOREDUCTASE / coproporphyrinogen oxidase / heme biosynthesis / enzyme | ||||||
Function / homology | Function and homology information coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / Heme biosynthesis / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Chromium sulfur SAD / Resolution: 2.4 Å | ||||||
Authors | Phillip, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of the oxygen-dependent coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae Authors: Phillips, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tlb.cif.gz | 404.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tlb.ent.gz | 333.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tlb_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 1tlb_full_validation.pdf.gz | 555.3 KB | Display | |
Data in XML | 1tlb_validation.xml.gz | 79.1 KB | Display | |
Data in CIF | 1tlb_validation.cif.gz | 110.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlb ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | odCPO forms a homodimer. 3 apparent biological dimers (six monomers) occupy the asymmetric unit of this crystal form. |
-Components
#1: Protein | Mass: 37535.230 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HEM13, YDR044W, YD5112.02 / Plasmid: pET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P11353, coproporphyrinogen oxidase #2: Chemical | ChemComp-SO4 / | #3: 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: 2.3 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.2 M Ammonium Sulfate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 29, 1998 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 83203 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5905 / Rsym value: 0.309 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: Chromium sulfur SAD / Resolution: 2.4→158.11 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.366 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.451 / ESU R Free: 0.305 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.507 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→158.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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