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Yorodumi- PDB-1kw1: Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kw1 | ||||||
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Title | Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with bound L-gulonate 6-phosphate | ||||||
Components | 3-Keto-L-Gulonate 6-Phosphate Decarboxylase | ||||||
Keywords | LYASE / beta/alpha-barrel | ||||||
Function / homology | Function and homology information 3-dehydro-L-gulonate-6-phosphate decarboxylase / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wise, E. / Yew, W.S. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Authors: Wise, E. / Yew, W.S. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kw1.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kw1.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kw1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1kw1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1kw1_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1kw1_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kw1 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kw1 | HTTPS FTP |
-Related structure data
Related structure data | 1kv8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 23603.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P39304, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 18% MePEG 5000, 50 mM bis-Tris propane, pH 7.0, 25 mM L-gulonate 6-phosphate. micro-batch at 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 274 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 1, 2001 / Details: mirrors |
Radiation | Monochromator: Gobel mirrors / 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→30 Å / Num. all: 35323 / Num. obs: 32215 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.4 / % possible all: 80 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 22847 / Num. measured all: 56895 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 77.9 % / Rmerge(I) obs: 0.099 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KV8 Resolution: 2.2→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |