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- PDB-6gpj: Crystal structure of human GDP-D-mannose 4,6-dehydratase in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gpj | ||||||
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Title | Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man | ||||||
![]() | GDP-mannose 4,6 dehydratase | ||||||
![]() | LYASE / GDP-mannose 4 / 6 dehydratase / fucosylation / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pfeiffer, M. / Krojer, T. / Johansson, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Nidetzky, B. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase. Authors: Pfeiffer, M. / Johansson, C. / Krojer, T. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.2 KB | Display | ![]() |
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PDB format | ![]() | 244 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 81.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gpkC ![]() 6gplC ![]() 6q94C ![]() 1t2aS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ADCB
#1: Protein | Mass: 40056.465 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 748 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/G4F.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/G4F.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-G4F / [[( #4: Chemical | ChemComp-NAP / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 -- 0.2M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→63.91 Å / Num. obs: 110446 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8103 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T2A Resolution: 1.94→63.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.445 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.16 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.493 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→63.9 Å
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Refine LS restraints |
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