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Yorodumi- PDB-1j93: Crystal Structure and Substrate Binding Modeling of the Uroporphy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j93 | ||||||
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Title | Crystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism | ||||||
Components | UROPORPHYRINOGEN DECARBOXYLASEUroporphyrinogen III decarboxylase | ||||||
Keywords | LYASE / beta barrel / plastidial enzyme / crystallographic dimer | ||||||
Function / homology | Function and homology information uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / chloroplast Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Martins, B.M. / Grimm, B. / Mock, H.-P. / Huber, R. / Messerschmidt, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism Authors: Martins, B.M. / Grimm, B. / Mock, H.-P. / Huber, R. / Messerschmidt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j93.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j93.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j93 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j93 | HTTPS FTP |
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-Related structure data
Related structure data | 1uroS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39187.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: Q42967, uroporphyrinogen decarboxylase | ||
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#2: Chemical | ChemComp-SO4 / #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: 3.14 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: ammonium sulfate, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 61 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 2, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→18 Å / Num. all: 257709 / Num. obs: 22173 / % possible obs: 97.7 % / Redundancy: 2.14 % / Rsym value: 0.06 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.3→18 Å / Redundancy: 3.95 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 257709 / Rsym value: 0.346 / % possible all: 98.3 |
Reflection | *PLUS Num. measured all: 257709 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Lowest resolution: 2.34 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.346 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1uro Resolution: 2.3→18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction option in CNS
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Refinement step | Cycle: LAST / Resolution: 2.3→18 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.209 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |