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Yorodumi- PDB-1z4n: Structure of beta-phosphoglucomutase with inhibitor bound alpha-g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z4n | ||||||
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Title | Structure of beta-phosphoglucomutase with inhibitor bound alpha-galactose 1-phosphate cocrystallized with Fluoride | ||||||
Components | Beta-phosphoglucomutase | ||||||
Keywords | ISOMERASE / Beta-phosphoglucomutase | ||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Tremblay, L.W. / Zhang, G. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Chemical Confirmation of a Pentavalent Phosphorane in Complex with beta-Phosphoglucomutase Authors: Tremblay, L.W. / Zhang, G. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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Remark 999 | SEQUENCE According to authors, the conflict in the sequence with the database has been mentioned ... SEQUENCE According to authors, the conflict in the sequence with the database has been mentioned in NCBI P71447 for the reference "Quain et al.,1997 Microbiology 143, 855-865". Authors received their clone from the same group. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z4n.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z4n.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1z4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z4n_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1z4n_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1z4n_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1z4n_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/1z4n ftp://data.pdbj.org/pub/pdb/validation_reports/z4/1z4n | HTTPS FTP |
-Related structure data
Related structure data | 1z4oC 1o08S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24239.594 Da / Num. of mol.: 2 / Fragment: isomerase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: pgmB / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase #2: Chemical | #3: Sugar | #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: 2.254 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 200 mM sodium acetate, 30% PEG 4000, 10 mM magnesium dicloride, 100 mM ammonium fluoride, 50 mM alpha-galactose 1-phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: osmic mirriors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→100 Å / Num. all: 31187 / Num. obs: 31187 / % possible obs: 95.3 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.6 / Num. unique all: 31017 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O08.pdb Resolution: 1.97→100 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): -1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→100 Å
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Refine LS restraints |
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Xplor file |
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