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Yorodumi- PDB-1q6q: Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q6q | ||||||
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Title | Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q6q.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q6q.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1q6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q6q_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 1q6q_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 1q6q_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1q6q_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6q ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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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) / Production host: Escherichia coli (E. coli) 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: 2.13 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 15% 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.695→100 Å / Num. obs: 49427 / % possible obs: 95.4 % / Observed criterion σ(I): 2.5 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.695→1.75 Å / Mean I/σ(I) obs: 5.8 / % possible all: 82.8 |
Reflection | *PLUS Highest resolution: 1.69 Å / Num. obs: 49731 / Num. measured all: 526555 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.69 Å / % possible obs: 82.8 % / Rmerge(I) obs: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.695→91.29 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.992 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: Engh & Huber / 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: 20.917 Å2
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Refinement step | Cycle: LAST / Resolution: 1.695→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.695→1.739 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 30 Å / Num. reflection obs: 47245 / Num. reflection Rfree: 2482 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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