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Yorodumi- PDB-2wvm: H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wvm | ||||||
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Title | H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in complex with GDP-alpha-D-Mannose and Mg(II) | ||||||
Components | MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE | ||||||
Keywords | TRANSFERASE / GT-A FOLD / GLYCOSYLTRANSFERASE / RETAINING MECHANISM / GLUCOSYL TRANSFERASE | ||||||
Function / homology | Function and homology information mannosyl-3-phosphoglycerate synthase activity / mannosylglycerate biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.977 Å | ||||||
Authors | Goncalves, S. / Borges, N. / Esteves, A.M. / Victor, B. / Soares, C.M. / Santos, H. / Matias, P.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural Analysis of Thermus Thermophilus Hb27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight Into the Retaining Mechanism of Glycosyltransferases. Authors: Goncalves, S. / Borges, N. / Esteves, A.M. / Victor, B. / Soares, C.M. / Santos, H. / Matias, P.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and Preliminary X-Ray Analysis of Mannosyl-3-Phosphoglycerate Synthase from Thermus Thermophilus Hb27 Authors: Goncalves, S. / Borges, N. / Santos, H. / Matias, P.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wvm.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvm.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wvm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2wvm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2wvm_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2wvm_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvm ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvm | HTTPS FTP |
-Related structure data
Related structure data | 2wvkC 2wvlSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.92177, 0.38769, 0.00651), Vector: |
-Components
#1: Protein | Mass: 43583.699 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA References: UniProt: Q72K30, mannosyl-3-phosphoglycerate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 3.6 Å3/Da / Density % sol: 65.7 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 AS AN ADDITIVE, 1-5 MM GDP-ALPHA-D-MANNOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.977→48.9 Å / Num. obs: 25598 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.977→3.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.09 / % possible all: 80.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WVL Resolution: 2.977→98.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 31.001 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.213 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.868 Å2
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Refinement step | Cycle: LAST / Resolution: 2.977→98.19 Å
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Refine LS restraints |
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