[English] 日本語
Yorodumi- PDB-1q6l: Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q6l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate | ||||||
Components | 3-keto-L-gulonate 6-phosphate decarboxylase | ||||||
Keywords | LYASE / BETA 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: 1.8 Å | ||||||
Authors | Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-l-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Authors: Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q6l.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q6l.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 1q6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q6l_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1q6l_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 1q6l_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1q6l_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6l ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-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) / Production host: Escherichia coli (E. coli) References: UniProt: P39304, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 16% MEPEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, Microbatch, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→91.2 Å / Num. all: 56895 / % possible obs: 91 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.3 Å2 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.099 / % possible all: 77.8 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 32215 / Num. measured all: 56895 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 77.8 % / Rmerge(I) obs: 0.099 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→91.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.876 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.735 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→91.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|