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Yorodumi- PDB-1r3y: Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-III -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r3y | ||||||
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Title | Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-III | ||||||
Components | Uroporphyrinogen Decarboxylase | ||||||
Keywords | LYASE / uroporphyrinogen decarboxylase coproporphyrinogen / X-ray crystallography | ||||||
Function / homology | Function and homology information porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.755 Å | ||||||
Authors | Phillips, J.D. / Whitby, F.G. / Kushner, J.P. / Hill, C.P. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase Authors: Phillips, J.D. / Whitby, F.G. / 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 | 1r3y.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r3y.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r3y_validation.pdf.gz | 860.2 KB | Display | wwPDB validaton report |
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Full document | 1r3y_full_validation.pdf.gz | 865.9 KB | Display | |
Data in XML | 1r3y_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1r3y_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/1r3y ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r3y | HTTPS FTP |
-Related structure data
Related structure data | 1r3qC 1r3rC 1r3sC 1r3tC 1r3vC 1r3wC 1uroS 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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1 |
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Unit cell |
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Details | URO-D is a dimer in solution and in the crystal. The dimer is formed by the 2-fold crystallographic rotation. |
-Components
#1: Protein | Mass: 40831.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06132, uroporphyrinogen decarboxylase |
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#2: Chemical | ChemComp-CP3 / |
#3: 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: 2.48 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 294 K / Method: liquid diffusion / pH: 6.5 Details: PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID ...Details: PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→87.71 Å / Num. all: 45954 / Num. obs: 45954 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.423 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1URO Resolution: 1.755→87.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.02 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.09 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.457 Å2
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Refinement step | Cycle: LAST / Resolution: 1.755→87.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.755→1.85 Å / Total num. of bins used: 10 /
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