+Open data
-Basic information
Entry | Database: PDB / ID: 2awd | ||||||
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Title | Crystal structure of LacC from Enterococcus faecalis | ||||||
Components | tagatose-6-phosphate kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information tagatose-6-phosphate kinase / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of LacC from Enterococcus faecalis Authors: Gorman, J. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2awd.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2awd.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 2awd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/2awd ftp://data.pdbj.org/pub/pdb/validation_reports/aw/2awd | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35397.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: lacC / Plasmid: modified pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q833W9, tagatose-6-phosphate kinase #2: Chemical | ChemComp-BR / #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: 2.56 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.4M NaCitrate, .1M Tris pH 8.5, cryo-Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2005 |
Radiation | Monochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 48795 / Num. obs: 48795 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.36 / Num. unique all: 4808 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.63 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 32.111 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.055 Å / Total num. of bins used: 20
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