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Yorodumi- PDB-1ga8: CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ga8 | |||||||||
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Title | CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DONOR AND ACCEPTOR SUGAR ANALOGS. | |||||||||
Components | GALACTOSYL TRANSFERASE LGTC | |||||||||
Keywords | TRANSFERASE / ALPHA-BETA PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Neisseria meningitidis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Persson, K. / Ly, H.D. / Diekelmann, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Authors: Persson, K. / Ly, H.D. / Dieckelmann, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ga8.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ga8.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ga8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1ga8 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1ga8 | HTTPS FTP |
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-Related structure data
Related structure data | 1g9rSC S: Starting model for refinement C: citing same article (ref.) |
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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: 36111.008 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: LGTC / Plasmid: PCW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P96945, UniProt: Q93EK7*PLUS, EC: 2.4.1.44 |
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#2: Polysaccharide | 4-deoxy-beta-D-xylo-hexopyranose-(1-4)-beta-D-glucopyranose / 4-deoxy-beta-lactose |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-UPF / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG monomethylether 2000, NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Details: used seeding | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 10, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 18508 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 8.1 / % possible all: 89.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 10 Å2 |
Reflection shell | *PLUS Mean I/σ(I) obs: 8.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1G9R Resolution: 2→24.38 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.83 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→24.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 18225 / Rfactor obs: 0.193 / Rfactor Rfree: 0.2276 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.223 / Rfactor Rwork: 0.189 |