+Open data
-Basic information
Entry | Database: PDB / ID: 4kep | |||||||||
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Title | Crystal structure of 4-pyridoxolactonase, wild-type | |||||||||
Components | 4-pyridoxolactonase | |||||||||
Keywords | HYDROLASE / alpha-beta/beta-alpha fold / lactone | |||||||||
Function / homology | Function and homology information 4-pyridoxolactonase / 4-pyridoxolactonase activity / vitamin B6 catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Mesorhizobium loti (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | |||||||||
Authors | Kobayashi, J. / Yoshikane, Y. / Baba, S. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of 4-pyridoxolactonase from Mesorhizobium loti. Authors: Kobayashi, J. / Yoshikane, Y. / Yagi, T. / Baba, S. / Mizutani, K. / Takahashi, N. / Mikami, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kep.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kep.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kep_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 4kep_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 4kep_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4kep_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/4kep ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4kep | HTTPS FTP |
-Related structure data
Related structure data | 3aj3SC 4keqC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30725.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6805 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988B9, 4-pyridoxolactonase |
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-Non-polymers , 6 types, 98 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-CL / | #7: 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: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. obs: 21861 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.65 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AJ3 Resolution: 1.83→36.144 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 21.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.45 Å2 / Biso mean: 29.1215 Å2 / Biso min: 15.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→36.144 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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