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Yorodumi- PDB-7b1k: Crystal structure of phosphatidyl serine synthase (PSS) in the cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b1k | ||||||
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Title | Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate. | ||||||
Components | CDP-diacylglycerol--serine O-phosphatidyltransferaseCDP-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 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 | 7b1k.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b1k.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 7b1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b1k ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b1k | HTTPS FTP |
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-Related 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: 24713.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (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 |
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-Non-polymers , 8 types, 50 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-OLC / ( #9: Water | ChemComp-HOH / | |
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-Details
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: 0.99989 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57 Å / Num. obs: 31163 / % possible obs: 97.67 % / Redundancy: 7.2 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.08 / Rrim(I) all: 0.22 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2098 / CC1/2: 0.39 / CC star: 0.75 / Rpim(I) all: 1.07 / Rrim(I) all: 2.9 / % possible all: 96.86 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→57 Å / SU ML: 0.3983 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.9602 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: 52.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→57 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: 15.7070834764 Å / Origin y: 78.1959094882 Å / Origin z: 114.090418272 Å
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Refinement TLS group | Selection details: all |