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Yorodumi- PDB-4lfk: Crystal Structure of D-galactose-6-phosphate isomerase in a subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lfk | ||||||
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Title | Crystal Structure of D-galactose-6-phosphate isomerase in a substrate-free form | ||||||
Components |
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Keywords | ISOMERASE / Rossmann-like alpha-beta-alpha sandwich fold / Rossmann Fold / Sugar-phosphate Binding / Isomerization | ||||||
Function / homology | Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta / : / : Function and homology information | ||||||
Biological species | Lactobacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Jung, W.S. / Pan, C.H. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates. Authors: Jung, W.S. / Singh, R.K. / Lee, J.K. / Pan, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lfk.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lfk.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/4lfk ftp://data.pdbj.org/pub/pdb/validation_reports/lf/4lfk | HTTPS FTP |
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-Related structure data
Related structure data | 4lflC 4lfmC 4lfnC 1nn4S 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
#1: Protein | Mass: 17884.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: lacA, LC705_00641 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7TGZ6, EC: 5.3.1.26 #2: Protein | Mass: 18889.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: lacB, LC705_00640 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7TGZ5, EC: 5.3.1.26 #3: 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: 2.34 Å3/Da / Density % sol: 47.4 % / Mosaicity: 0.381 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2M potassium formate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97932 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→50 Å / Num. obs: 50182 / % possible obs: 99.7 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.073 / Χ2: 0.994 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NN4 Resolution: 1.96→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2
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Solvent computation | Bsol: 13.4704 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.56 Å2 / Biso mean: 21.3874 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→50 Å
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Refine LS restraints |
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Xplor file |
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