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Yorodumi- PDB-6gpl: Crystal structure of human GDP-D-mannose 4,6-dehydratase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gpl | ||||||
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Title | Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man | ||||||
Components | GDP-mannose 4,6 dehydratase | ||||||
Keywords | LYASE / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å | ||||||
Authors | Pfeiffer, M. / Krojer, T. / Johansson, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Nidetzky, B. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Acs Catalysis / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gpl.cif.gz | 311.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gpl.ent.gz | 248.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gpl ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gpl | HTTPS FTP |
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-Related 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 ensembles :
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-Components
-Protein , 1 types, 4 molecules BCDE
#1: Protein | Mass: 40056.465 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Production host: Escherichia coli (E. coli) / References: UniProt: O60547, GDP-mannose 4,6-dehydratase |
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-Non-polymers , 5 types, 904 molecules
#2: Chemical | ChemComp-BCN / | ||||||
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#3: Chemical | ChemComp-F7E / [[( #4: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% PEG6000, 0.1M bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→39.09 Å / Num. obs: 151973 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.76→1.81 Å / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Resolution: 1.76→39.09 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.623 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.098 / 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: 28.03 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→39.09 Å
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Refine LS restraints |
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