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Yorodumi- PDB-5z9o: The crystal structure of Cyclopropane-fatty-acyl-phospholipid syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z9o | |||||||||
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Title | The crystal structure of Cyclopropane-fatty-acyl-phospholipid synthase from Lactobacillus acidophilus | |||||||||
Components | Cyclopropane-fatty-acyl-phospholipid synthase | |||||||||
Keywords | TRANSFERASE / Cyclopropane-fatty-acyl-phospholipid synthase / phosphatidyl ethanolamine / bicarbonate ion / carbocation mechanism / LIPID BINDING PROTEIN | |||||||||
Function / homology | Function and homology information cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / lipid biosynthetic process / methylation Similarity search - Function | |||||||||
Biological species | Lactobacillus acidophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Pan, C.L. / Ma, Y.L. / Wang, Q.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Biochem. / Year: 2019 Title: Crystal structure of bacterial cyclopropane-fatty-acyl-phospholipid synthase with phospholipid. Authors: Ma, Y. / Pan, C. / Wang, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z9o.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z9o.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z9o_validation.pdf.gz | 890.6 KB | Display | wwPDB validaton report |
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Full document | 5z9o_full_validation.pdf.gz | 916.7 KB | Display | |
Data in XML | 5z9o_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 5z9o_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z9o ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z9o | HTTPS FTP |
-Related structure data
Related structure data | 1l1eS S: Starting model for refinement |
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Similar structure data |
-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: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 4 - 389 / Label seq-ID: 4 - 389
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-Components
#1: Protein | Mass: 46030.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) (bacteria) Strain: ATCC 700396 / NCK56 / N2 / NCFM / Gene: LBA1274 / Production host: Escherichia coli (E. coli) References: UniProt: Q5FJM0, cyclopropane-fatty-acyl-phospholipid synthase #2: Chemical | #3: Chemical | #4: 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: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 1.5 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dehydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→88.21 Å / Num. obs: 37057 / % possible obs: 99.94 % / Redundancy: 4.3 % / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.703→2.773 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L1E Resolution: 2.7→44.106 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.335 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 49.138 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→44.106 Å
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Refine LS restraints |
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