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Yorodumi- PDB-7b1n: Crystal structure of phosphatidyl serine synthase (PSS) in the cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b1n | |||||||||
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Title | Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate. | |||||||||
Components | CDP-diacylglycerol--serine O-phosphatidyltransferase | |||||||||
Keywords | LIPID BINDING PROTEIN / Membrane protein / Lipid synthase | |||||||||
Function / homology | Function and homology information CDP-diacylglycerol-serine O-phosphatidyltransferase / CDP-diacylglycerol-serine O-phosphatidyltransferase activity / phospholipid biosynthetic process / plasma membrane Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | |||||||||
Authors | Yildiz, O. / Centola, M. | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases Authors: Centola, M. / Betz, H. / Yildiz, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b1n.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b1n.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 7b1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b1n_validation.pdf.gz | 882 KB | Display | wwPDB validaton report |
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Full document | 7b1n_full_validation.pdf.gz | 900.2 KB | Display | |
Data in XML | 7b1n_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7b1n_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b1n ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b1n | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24713.398 Da / Num. of mol.: 2 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: pssA, MJ1212 / Production host: Escherichia coli (E. coli) References: UniProt: Q58609, CDP-diacylglycerol-serine O-phosphatidyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 300 K / Method: lipidic cubic phase Details: Qiagens MBclass Suit and MBclass Suit II Molecular Dimension MemGold |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 19466 / % possible obs: 99.12 % / Redundancy: 6.2 % / Biso Wilson estimate: 61.44 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.107 / Rrim(I) all: 0.266 / Net I/σ(I): 4.51 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 1017 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.864 / Rrim(I) all: 2.11 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→46.7 Å / SU ML: 0.4192 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 44.2951 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 69.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.4882236554 Å / Origin y: -28.0331962376 Å / Origin z: 17.9739046946 Å
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Refinement TLS group | Selection details: all |