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- PDB-1jpk: Gly156Asp mutant of Human UroD, human uroporphyrinogen III decarb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jpk | ||||||
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Title | Gly156Asp mutant of Human UroD, human uroporphyrinogen III decarboxylase | ||||||
![]() | UROPORPHYRINOGEN DECARBOXYLASE | ||||||
![]() | LYASE / heme biosynthesis | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Phillips, J.D. / Parker, T.L. / Schubert, H.L. / Whitby, F.G. / Hill, C.P. / Kushner, J.P. | ||||||
![]() | ![]() Title: Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase. Authors: Phillips, J.D. / Parker, T.L. / Schubert, H.L. / Whitby, F.G. / Hill, C.P. / Kushner, J.P. #1: ![]() Title: Crystal Structure of Human Uroporphyrinogen Decarboxylase Authors: Whitby, F.G. / Phillips, J.D. / Kushner, J.P. / Hill, C.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 432.1 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jphC ![]() 1jpiC ![]() 1uroS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | physiological dimer, monomer in the ASU |
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Components
#1: Protein | Mass: 43423.531 Da / Num. of mol.: 1 / Mutation: G156D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD and MES, or CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 / Details: Phillips, J.D., (1997) Protein Sci., 6, 1343. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 22708 / Num. obs: 22708 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.84 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.39 / % possible all: 99.2 |
Reflection | *PLUS Num. obs: 23423 / Num. measured all: 274282 |
Reflection shell | *PLUS % possible obs: 99.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1URO Resolution: 2.2→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.3 Å |