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Yorodumi- PDB-7ntg: Bdellovibrio bacteriovorus PGI in complex with fructose-6-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ntg | ||||||
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Title | Bdellovibrio bacteriovorus PGI in complex with fructose-6-phosphate | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / Glucose-6-phosphate isomerase Isomerase Phosphoglucose isomerase | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å | ||||||
Authors | Meek, R.W. / Lovering, A.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2021 Title: Bdellovibrio bacteriovorus phosphoglucose isomerase structures reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding. Authors: Meek, R.W. / Cadby, I.T. / Lovering, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ntg.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ntg.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ntg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ntg_validation.pdf.gz | 823.8 KB | Display | wwPDB validaton report |
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Full document | 7ntg_full_validation.pdf.gz | 824.6 KB | Display | |
Data in XML | 7ntg_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 7ntg_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/7ntg ftp://data.pdbj.org/pub/pdb/validation_reports/nt/7ntg | HTTPS FTP |
-Related structure data
Related structure data | 7nssSC 7o0aC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48055.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria) Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: pgi, Bd0741 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MPU9, glucose-6-phosphate isomerase |
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#2: Chemical | ChemComp-F6R / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M ammonium acetate 0.1 M sodium acetate pH 5.0 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→43.82 Å / Num. obs: 52651 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 41.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 19.4 % / Rmerge(I) obs: 1.966 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3855 / CC1/2: 0.822 / Rpim(I) all: 0.655 / Rrim(I) all: 2.073 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NSS Resolution: 1.67→43.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.4 Å2 / Biso mean: 36.123 Å2 / Biso min: 22.29 Å2
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Refinement step | Cycle: final / Resolution: 1.67→43.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.654→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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