[English] 日本語
Yorodumi- PDB-6hdg: D170N variant of beta-phosphoglucomutase from Lactococcus lactis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hdg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | D170N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with beta-G1P in a closed conformer to 1.2 A. | |||||||||
Components | Beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / 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 subsp. lactis (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Wood, H.P. / Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: To Be Published Title: Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase. Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6hdg.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6hdg.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hdg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6hdg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6hdg_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6hdg_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hdg ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hdg | HTTPS FTP |
-Related structure data
Related structure data | 6h8uC 6h8vC 6h8wC 6h8xC 6h8yC 6h8zC 6h90C 6h93C 6h94C 6hdfC 6hdhC 6hdiC 6hdjC 6hdkC 6hdlC 6hdmC 2wf5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24238.607 Da / Num. of mol.: 1 / Mutation: K125R, Y206H, D170N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase | ||||
---|---|---|---|---|---|
#2: Sugar | ChemComp-XGP / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→48.86 Å / Num. obs: 78880 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.986 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3894 / CC1/2: 0.562 / Rpim(I) all: 0.634 / Rrim(I) all: 2.087 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WF5 Resolution: 1.15→48.86 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.416 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.394 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.15→48.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|