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- PDB-2c5a: GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c5a | ||||||
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Title | GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site | ||||||
![]() | GDP-MANNOSE-3', 5'-EPIMERASE | ||||||
![]() | ISOMERASE / 3' 5'-EPIMERASE / SHORT CHAIN DEHYDRATASE/REDUCTASE / GDP-MANNOSE / GDP-GULOSE / GDP-GALACTOSE / KETO INTERMEDIATE / VITAMIN C / SDR / ASCORBATE BIOSYNTHESIS / NAD | ||||||
Function / homology | ![]() GDP-mannose 3,5-epimerase / GDP-mannose 3,5-epimerase activity / L-ascorbic acid biosynthetic process / plastid / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Major, L.L. / Wolucka, B.A. / Naismith, J.H. | ||||||
![]() | ![]() Title: Structure and Function of Gdp-Mannose-3',5'-Epimerase: An Enzyme which Performs Three Chemical Reactions at the Same Active Site. Authors: Major, L.L. / Wolucka, B.A. / Naismith, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358 KB | Display | ![]() |
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PDB format | ![]() | 289.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c54SC ![]() 2c59C ![]() 2c5eC S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42927.602 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: GDP-BETA-L-GALACTOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GALACTOSE-MONOPHOSPHATE (GA3), LINKING THE GDP O3A TO THE GA3 PB Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1040 molecules ![](data/chem/img/GDC.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-BTB / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYZES A REVERSIBLE EPIMERIZATION OF GDP-D-MANNOSE ENGINEERED RESIDUE IN CHAIN A, TYR 174 TO PHE ...CATALYZES A REVERSIBLE |
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Sequence details | THE FIRST TWO RESIDUES (GA) IN THE SPECIFIED SEQUENCE ARE A REMNANT FROM A CLEAVED HIS-TAG (AND ARE ...THE FIRST TWO RESIDUES (GA) IN THE SPECIFIED SEQUENCE ARE A REMNANT FROM A CLEAVED HIS-TAG (AND ARE NOT IN THE UNIPROT SEQUENCE), THE RESIDUE NUMBERING IN THE STRUCTURE USES THE THIRD RESIDUE (M) AS RESIDUE 1. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 100 MM BIS-TRIS PH 6.0, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→23.12 Å / Num. obs: 126826 / % possible obs: 96.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.5 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C54 Resolution: 1.4→21.61 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.472 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.049 / Stereochemistry target values: RESTRAINED Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH MONOMER OF GME Y174F CONTAINS A NAD IN THE NUCLEOTIDE BINDING SITE, AND GDP-BETA-L-GALACTOSE IN THE NUCLEOTIDE SUGAR BINDING SITE.
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→21.61 Å
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Refine LS restraints |
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