+Open data
-Basic information
Entry | Database: PDB / ID: 7cnw | |||||||||
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Title | Crystal structure of Apo PSD from E. coli (1.90 A) | |||||||||
Components |
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Keywords | LYASE / Phosphatidylserine decarboxylase / pyruvoyl-dependent decarboxylase / auto-cleaved / serine protease / MEMBRANE PROTEIN | |||||||||
Function / homology | phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase / Phosphatidylserine decarboxylase, prokaryotic type 1 / Phosphatidylserine decarboxylase / phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / plasma membrane / Phosphatidylserine decarboxylase proenzyme Function and homology information | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | Kim, J. / Cho, G. | |||||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Sci Rep / Year: 2021 Title: Structural insights into phosphatidylethanolamine formation in bacterial membrane biogenesis. Authors: Cho, G. / Lee, E. / Kim, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cnw.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cnw.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/7cnw ftp://data.pdbj.org/pub/pdb/validation_reports/cn/7cnw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 28645.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: psd, FAZ83_09855 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A6D2XQZ0, phosphatidylserine decarboxylase #2: Protein/peptide | Mass: 4482.063 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: psd, FAZ83_09855 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A6D2XQZ0, phosphatidylserine decarboxylase #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 3.43 Å3/Da / Density % sol: 64.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.1 M BIS-TRIS pH 6.3, 28% w/v PEGMME 2000, 5% w/v 1.6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.98011 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 29, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→49.03 Å / Num. obs: 71625 / % possible obs: 98.8 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.037 / Rrim(I) all: 0.142 / Net I/σ(I): 14.6 / Num. measured all: 1009308 / Scaling rejects: 2 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→41.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.333 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.124 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.39 Å2 / Biso mean: 39.495 Å2 / Biso min: 15.18 Å2
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Refinement step | Cycle: final / Resolution: 1.9→41.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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