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- PDB-2x60: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x60 | ||||||
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Title | Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP. | ||||||
![]() | MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / NUCLEOTIDYL TRANSFERASE | ||||||
Function / homology | ![]() mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
![]() | ![]() Title: Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase and its Regulation by Divalent Ions. Authors: Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.6 KB | Display | ![]() |
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PDB format | ![]() | 117.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x5sSC ![]() 2x5zC ![]() 2x65C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38655.359 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X0C3, mannose-1-phosphate guanylyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 261 TO LEU ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | pH: 5 Details: 100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 200 MM CALCIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→67.6 Å / Num. obs: 17147 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X5S Resolution: 2.8→67.57 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 41.34 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→67.57 Å
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Refine LS restraints |
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