[English] 日本語
Yorodumi- PDB-4lul: The crystal structure of the P132A, Y133D mutant of Pyrococcus fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lul | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the P132A, Y133D mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese. | ||||||
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: 1.89 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lul.cif.gz | 164 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lul.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lul_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lul_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 4lul_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 4lul_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4lul ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4lul | HTTPS FTP |
-Related structure data
Related structure data | 4ltaC 4lukC 4lumC 1x7nS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the biological dimer. |
-Components
#1: Protein | Mass: 21431.312 Da / Num. of mol.: 2 / Mutation: P132A, Y133D 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.01 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M calcium acetate, 0.1 M sodium acetate PH6.5, 40% PEG300., VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.89→25.85 Å / Num. all: 29381 / Num. obs: 29381 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.89→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2144 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X7N Resolution: 1.89→25.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.206 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 33.754 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→25.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.895→1.944 Å / Total num. of bins used: 20
|