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Yorodumi- PDB-2gt4: Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gt4 | ||||||
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Title | Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex with GDP-mannose and MG+2 | ||||||
Components | GDP-mannose mannosyl hydrolase | ||||||
Keywords | HYDROLASE / GDP-mannose hydrolase GDP-glucose hydrolase NUDIX GDP GDP-fucose | ||||||
Function / homology | Function and homology information GDP-glucosidase activity / GDP-mannose mannosyl hydrolase activity / lipopolysaccharide biosynthetic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / manganese ion binding / magnesium ion binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Gabelli, S.B. / Bianchet, M.A. / Azurmendi, H.F. / Mildvan, A.S. / Amzel, L.A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-mannose mannosyl hydrolase reaction. Authors: Gabelli, S.B. / Azurmendi, H.F. / Bianchet, M.A. / Amzel, L.M. / Mildvan, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gt4.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gt4.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gt4_validation.pdf.gz | 615.9 KB | Display | wwPDB validaton report |
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Full document | 2gt4_full_validation.pdf.gz | 624.9 KB | Display | |
Data in XML | 2gt4_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 2gt4_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/2gt4 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/2gt4 | HTTPS FTP |
-Related structure data
Related structure data | 2gt2C 1ryaS 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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2 |
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Unit cell |
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Details | biological assembly is a dimer (A,B) C forms a dimer with its symmetry related partner using the 2 fold |
-Components
#1: Protein | Mass: 18408.627 Da / Num. of mol.: 3 / Mutation: Y103F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k12 / Gene: yefc / Plasmid: pet11b / Production host: Escherichia coli (E. coli) References: UniProt: P32056, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | #3: Chemical | #4: Sugar | #5: 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: 3.87 Å3/Da / Density % sol: 68.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 5mM GDP-mannose 5mM glucose 5mM GDP-mannose 5mM glucose 100 mM Tris HCL p8.5 20% PEG 4000, 0.2 Mg Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 36595 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.072 / Χ2: 2.814 / Net I/σ(I): 14.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYA Resolution: 2.3→77.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.243 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.223 / ESU R Free: 0.19 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.589 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→77.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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