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Yorodumi- PDB-4rfl: Crystal structure of G1PDH with NADPH from Methanocaldococcus jan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rfl | ||||||
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Title | Crystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii | ||||||
Components | Glycerol-1-phosphate dehydrogenase [NAD(P)+] | ||||||
Keywords | OXIDOREDUCTASE / Rossman fold Metal Ion Binding / Dehydrogenase / NADP(H) binding / sn-glycerol-1-phosphate dehydrogenase | ||||||
Function / homology | Function and homology information glycerol-1-phosphate dehydrogenase (NAD+) activity / glycerol-1-phosphate dehydrogenase (NADP+) activity / sn-glycerol-1-phosphate dehydrogenase / glycerophospholipid metabolic process / phospholipid biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Carbone, V. / Ronimus, R.S. / Schofield, L.R. / Sutherland-Smith, A.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase. Authors: Carbone, V. / Schofield, L.R. / Zhang, Y. / Sang, C. / Dey, D. / Hannus, I.M. / Martin, W.F. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rfl.cif.gz | 286.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rfl.ent.gz | 229.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rfl_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4rfl_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4rfl_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 4rfl_validation.cif.gz | 74.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/4rfl ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rfl | HTTPS FTP |
-Related structure data
Related structure data | 4rgqC 4rgvC 3ce9S 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: Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 2 - 335 / Label seq-ID: 38 - 371
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41462.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: egsA, MJ0712 / Plasmid: pET100D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) References: UniProt: Q58122, sn-glycerol-1-phosphate dehydrogenase |
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-Non-polymers , 6 types, 467 molecules
#2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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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: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 294 K / pH: 8.5 Details: 30% (v/v) P550MME/P20K, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9116 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2013 |
Radiation | Monochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.68 Å / Num. obs: 78703 / % possible obs: 98.3 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CE9 Resolution: 2.2→46.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.164 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.195 / 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: 34.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.269 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.68 Å
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Refine LS restraints |
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