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Yorodumi- PDB-5kym: Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kym | ||||||
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Title | Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima | ||||||
Components | 1-acyl-sn-glycerol-3-phosphate acyltransferase | ||||||
Keywords | TRANSFERASE / integral membrane / membrane helices / HX4D acyltransferase / alpha-beta structure / 1-acyl-sn-glycerol-3-phosphate acyltransferase | ||||||
Function / homology | Function and homology information 1-acylglycerol-3-phosphate O-acyltransferase / 1-acylglycerol-3-phosphate O-acyltransferase activity / phosphatidic acid biosynthetic process / phospholipid biosynthetic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Robertson, R.M. / Yao, J. / Gajewski, S. / Kumar, G. / Martin, E.W. / Rock, C.O. / White, S.W. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: A two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer. Authors: Robertson, R.M. / Yao, J. / Gajewski, S. / Kumar, G. / Martin, E.W. / Rock, C.O. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kym.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kym.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5kym ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5kym | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 244 / Label seq-ID: 1 - 244
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-Components
#1: Protein | Mass: 28743.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1701 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: R4NS39, UniProt: Q9X219*PLUS, 1-acylglycerol-3-phosphate O-acyltransferase #2: Chemical | ChemComp-HGX / #3: Chemical | #4: Sugar | ChemComp-LMT / | #5: 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: 3.81 Å3/Da / Density % sol: 67.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-22% (w/v) polyethylene glycol 3350 (PEG3350), 0.1 M HEPES, and 0.2 M MgCl 2 PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 7, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.46 Å / Num. obs: 21613 / % possible obs: 99.94 % / Redundancy: 9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1879 / Net I/σ(I): 10.18 |
Reflection shell | Resolution: 2.802→2.901 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.167 / % possible all: 99.58 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→46.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.872 / SU B: 40.064 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.363 / 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: 79.442 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→46.46 Å
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Refine LS restraints |
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