+Open data
-Basic information
Entry | Database: PDB / ID: 4q7c | ||||||
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Title | Structure of AF2299, a CDP-alcohol phosphotransferase | ||||||
Components | AF2299, a CDP-alcohol phosphotransferase | ||||||
Keywords | TRANSFERASE / CDP-alcohol phosphotransferase / membrane protein / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS | ||||||
Function / homology | Function and homology information phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å | ||||||
Authors | Clarke, O.B. / Sciara, G. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Shapiro, L. / Mancia, F. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Structural basis for catalysis in a CDP-alcohol phosphotransferase. Authors: Sciara, G. / Clarke, O.B. / Tomasek, D. / Kloss, B. / Tabuso, S. / Byfield, R. / Cohn, R. / Banerjee, S. / Rajashankar, K.R. / Slavkovic, V. / Graziano, J.H. / Shapiro, L. / Mancia, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7c.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7c.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7c ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7c | HTTPS FTP |
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-Related structure data
Related structure data | 4o6mSC 4o6nC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42260.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: AF2299, AF_2299 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: O27985 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MPG / [( #4: Chemical | #5: Chemical | |
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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: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 7 Details: 15% PEG 550 MME, 0.1 M Na-HEPES pH 7.0, 0.2 M potassium sodium tartrate, 2.5 mM CDP-glycerol, 1 mM TCEP, Lipidic cubic phase (LCP), temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.0245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0245 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→100 Å / Num. all: 31012 / Num. obs: 31012 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.98 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4O6M Resolution: 3.102→69.128 Å / SU ML: 0.46 / σ(F): 0.03 / Phase error: 27.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6475 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.102→69.128 Å
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Refine LS restraints |
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LS refinement shell |
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