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Yorodumi- PDB-7drk: Crystal structure of phosphatidylglycerol phosphate synthase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7drk | |||||||||
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Title | Crystal structure of phosphatidylglycerol phosphate synthase in complex with cytidine diphosphate-diacylglycerol | |||||||||
Components | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | |||||||||
Keywords | TRANSFERASE / Substrate complex / Phospholipid synthase / Staphylococcus aureus / Transferase. | |||||||||
Function / homology | Function and homology information CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase / CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity / phosphatidylglycerol biosynthetic process / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Yang, B.W. / Liu, Z.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Curr Res Struct Biol / Year: 2021 Title: The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. Authors: Yang, B. / Yao, H. / Li, D. / Liu, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7drk.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7drk.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 7drk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7drk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7drk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7drk_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 7drk_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7drk ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7drk | HTTPS FTP |
-Related structure data
Related structure data | 7drjSC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23199.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper ...Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin. Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria) Gene: pgsA, SA1126 / Plasmid: pET-15b Details (production host): Ampicillin resistance; the pET-15b vector carries an N-terminal His-Tag sequence followed by a thrombin site and three cloning sites. Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 References: UniProt: P63756, CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase |
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-Non-polymers , 7 types, 130 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-G3P / #5: Chemical | #6: Chemical | ChemComp-BU1 / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.07 Å3/Da / Density % sol: 59.88 % / Description: Plate-like crystal |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 15-26% (v/v) 1,4-butanediol, 0.2M zinc acetate, 0.1M imidazole/HCl (pH 5.0-7.5) PH range: 5.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2019 |
Radiation | Monochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→35 Å / Num. obs: 11858 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 58.93 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.89→3.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2344 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DRJ Resolution: 3→9.99 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.23 / 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 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→9.99 Å
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Refine LS restraints |
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LS refinement shell |
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