+Open data
-Basic information
Entry | Database: PDB / ID: 3gvw | ||||||
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Title | Single-chain UROD F217Y (YF) mutation | ||||||
Components | Uroporphyrinogen decarboxylase | ||||||
Keywords | LYASE / uroporphyrinogen / decarboxylase / heme biosynthesis / Acetylation / Cytoplasm / Disease mutation / Phosphoprotein / Porphyrin biosynthesis | ||||||
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 / Resolution: 2.8 Å | ||||||
Authors | Hill, C.P. / Phillips, J.D. / Whitby, F.G. / Warby, C. / Kushner, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen. Authors: Phillips, J.D. / Warby, C.A. / 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 | 3gvw.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gvw.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gvw_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 3gvw_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 3gvw_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3gvw_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvw ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40847.766 Da / Num. of mol.: 1 / Mutation: F217Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06132, uroporphyrinogen decarboxylase |
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#2: 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: 2.69 Å3/Da / Density % sol: 54.34 % |
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Crystal grow | Method: hanging drop / Details: hanging drop |
-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: Aug 18, 2008 / Details: yale mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.5 % / Av σ(I) over netI: 19.75 / Number: 83299 / Rmerge(I) obs: 0.086 / Χ2: 1.03 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 11174 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.8→40 Å / Num. obs: 11174 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Χ2: 1.032 / Net I/σ(I): 19.754 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.8→33.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.784 / SU B: 16.09 / SU ML: 0.319 / SU Rfree: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE SECOND OF THE TWO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE SECOND OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, WE HAVE MODELED Y217 IN TWO CONFORMATIONS AT ONE-HALF OCCUPANCY EACH. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 217 IS EFFECTIVELY HALF F AND HALF Y.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.62 Å2 / Biso mean: 70.948 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→33.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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