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Yorodumi- PDB-4luk: The crystal structure of the P132A, Y133G mutant of Pyrococcus fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4luk | ||||||
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Title | The crystal structure of the P132A, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate. | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / Cupin Fold / Glucose 6-phsphate and Fructose 6-phosphate binding protein | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Baker, P.J. / Almourfi, F.M. | ||||||
Citation | Journal: To be Published Title: Correlated mutation analysis as a tool for smart library design to improve protein performance. Authors: Baker, P.J. / Almourfi, F.M. / Raedts, J. / Joosten, H.-J. / Hendriks, S. / Kengen, S.W.M. / Hage, W.R. / Schaap, P.J. / Sedelnikova, S.E. / Van der Oost, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4luk.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4luk.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 4luk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4luk_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 4luk_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 4luk_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4luk_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4luk ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4luk | HTTPS FTP |
-Related structure data
Related structure data | 4ltaC 4lulC 4lumC 1x7nS C: citing same article (ref.) 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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Details | The second part of the biological assembly is generated by the two fold axis: -X, Y, -Z |
-Components
#1: Protein | Mass: 21373.275 Da / Num. of mol.: 1 / Mutation: P132A, Y133G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: pgiA, PF0196 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83194, glucose-6-phosphate isomerase | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Sugar | ChemComp-PA5 / | ||
#4: Chemical | ChemComp-EDO / #5: 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: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.35 M MgCl2, 0.1 M sodium acetate PH 5.5 and 19% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2011 / Details: Diamond IO3 |
Radiation | Monochromator: Diamond IO3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→28.92 Å / Num. all: 32797 / Num. obs: 32797 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.41→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1460 / % possible all: 55.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X7N Resolution: 1.41→28.92 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.172 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.299 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→28.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.406→1.443 Å / Total num. of bins used: 20
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