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Yorodumi- PDB-2q71: Uroporphyrinogen Decarboxylase G168R single mutant enzyme in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q71 | ||||||
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Title | Uroporphyrinogen Decarboxylase G168R single mutant enzyme in complex with coproporphyrinogen-III | ||||||
Components | Uroporphyrinogen decarboxylase | ||||||
Keywords | LYASE / Uroporphyrinogen Decarboxylase enzyme UROD G168R coproporphyrinogen-III product complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Phillips, J.D. / Whitby, F.G. / Stadtmueller, B.M. / Edwards, C.Q. / Hill, C.P. / Kushner, J.P. | ||||||
Citation | Journal: Transl.Res. / Year: 2007 Title: Two Novel Uropophyrinogen Decarboxylase (URO-D) Mutations Causing Hepatoerythropoietic Porphyria (HEP) Authors: Phillips, J.D. / Whitby, F.G. / Stadtmueller, B.M. / Edwards, C.Q. / Hill, C.P. / Kushner, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q71.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q71.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 2q71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q71_validation.pdf.gz | 855.3 KB | Display | wwPDB validaton report |
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Full document | 2q71_full_validation.pdf.gz | 860.4 KB | Display | |
Data in XML | 2q71_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 2q71_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q71 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q71 | HTTPS FTP |
-Related structure data
Related structure data | 2q6zC 1ry3S C: citing same article (ref.) S: Starting model for refinement |
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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 | The crystal contains one monomer per asymmetric unit. The functional enzyme is a dimer of identical subunits. A crystallographic 2-fold generates teh biologically functional dimeric enzyme. The two identical active sites have been shown to act independently. One reaction product molecule (copropophyrinogen-III) is in the active site. |
-Components
#1: Protein | Mass: 39862.770 Da / Num. of mol.: 1 / Mutation: G168R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3-pLysS / 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: 2.76 Å3/Da / Density % sol: 55.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protien at 6.5 mg/ml in 50mM Tris, pH 7.5, 1mM BME was mixed 5 parts to 3 parts of precipitant (1.7M citrate, pH 7.0) and equilibrated by sitting drop vapor diffusion against a well of ...Details: Protien at 6.5 mg/ml in 50mM Tris, pH 7.5, 1mM BME was mixed 5 parts to 3 parts of precipitant (1.7M citrate, pH 7.0) and equilibrated by sitting drop vapor diffusion against a well of precipitant., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: Sep 19, 2003 / Details: Yale focusing mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Yale Focusing mirrors, 1.5418 angstrom wavelength, 67 degrees of 0.5 degree oscillations (134 images, 0-67 degrees) plus 12 degrees of 0.25 degree oscillations (48 images 65-77 degrees) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 32683 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Χ2: 1.004 / Net I/σ(I): 11.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ry3 Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.943 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALS WERE ISOMORPHOUS TO 1RY3.
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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: 27.004 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.951 Å / Total num. of bins used: 20
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