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- PDB-1r3q: Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-I -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r3q | ||||||
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Title | Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-I | ||||||
![]() | Uroporphyrinogen Decarboxylase | ||||||
![]() | LYASE / uroporphyrinogen decarboxylase coproporphyrinogen / X-ray crystallography | ||||||
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. / Whitby, F.G. / Kushner, J.P. / Hill, C.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.4 KB | Display | ![]() |
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PDB format | ![]() | 70.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 873.5 KB | Display | ![]() |
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Full document | ![]() | 878.5 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r3rC ![]() 1r3sC ![]() 1r3tC ![]() 1r3vC ![]() 1r3wC ![]() 1r3yC ![]() 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 | The asymmetric unit contains one URO-D monomer. URO-D is a dimer. The dimer is formed by the crystallographic 2-fold operator. |
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Components
#1: Protein | Mass: 40831.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-1CP / |
#3: Chemical | ChemComp-CO2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: liquid diffusion / pH: 6.5 Details: Crystallization of URO-D in complex with coproporphyrinogen required crystallization in an anaerobic chamber with PBG and PBG-D added to the solution for the generation of uroporphyrinogen ...Details: Crystallization of URO-D in complex with coproporphyrinogen required crystallization in an anaerobic chamber with PBG and PBG-D added to the solution for the generation of uroporphyrinogen in-situ. URO-D was active under these conditions, creating coproporphyrinogen. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop / 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: 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: 1.7→30 Å / Num. all: 50593 / Num. obs: 50593 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.485 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.7 Å / % possible obs: 99.6 % / Num. measured all: 270866 |
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1URO Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.724 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / 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: 25.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→87.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.792 Å / Total num. of bins used: 10 /
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Software | *PLUS Version: 5.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å |