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Yorodumi- PDB-1l7j: X-ray structure of galactose mutarotase from Lactococcus lactis (apo) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l7j | ||||||
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Title | X-ray structure of galactose mutarotase from Lactococcus lactis (apo) | ||||||
Components | galactose mutarotase | ||||||
Keywords | ISOMERASE / mutarotase / epimerase / galactose metabolism | ||||||
Function / homology | Function and homology information aldose 1-epimerase / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.9 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: High resolution X-ray structure of galactose mutarotase from Lactococcus lactis. Authors: Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l7j.cif.gz | 161.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l7j.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 1l7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7j_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 1l7j_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 1l7j_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1l7j_validation.cif.gz | 60.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7j ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7j | HTTPS FTP |
-Related 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: 38622.957 Da / Num. of mol.: 2 / Mutation: E2S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: GALM / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9ZB17, aldose 1-epimerase #2: 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: 2.16 Å3/Da / Density % sol: 43.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG-5000-O-Methylether, MES, NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 9, 2002 / Details: goebel mirrors |
Radiation | Monochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 49650 / Num. obs: 49650 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.081 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5683 / Rsym value: 0.18 / % possible all: 86.7 |
Reflection | *PLUS Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 86.7 % / Num. unique obs: 5683 / Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 44968 / Rfactor all: 0.197 / Rfactor obs: 0.189 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.189 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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