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Yorodumi- PDB-3hsi: Crystal structure of phosphatidylserine synthase Haemophilus infl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hsi | ||||||
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Title | Crystal structure of phosphatidylserine synthase Haemophilus influenzae Rd KW20 | ||||||
Components | Phosphatidylserine synthaseCDP-diacylglycerol—serine O-phosphatidyltransferase | ||||||
Keywords | TRANSFERASE / Haemophilus influenzae / phosphatidylserine synthase / CDP-diacylglycerol--serine O-phosphatidyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Cell inner membrane / Cell membrane / Membrane / Phospholipid biosynthesis | ||||||
Function / homology | Function and homology information CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity / CDP-diacylglycerol-serine O-phosphatidyltransferase / CDP-diacylglycerol-serine O-phosphatidyltransferase activity / cardiolipin biosynthetic process / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Chang, C. / Li, H. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphatidylserine synthase Haemophilus influenzae Rd KW20 Authors: Chang, C. / Li, H. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hsi.cif.gz | 287.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hsi.ent.gz | 241.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hsi ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hsi | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53654.332 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: pssA, HI0425 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic References: UniProt: P44704, CDP-diacylglycerol-serine O-phosphatidyltransferase #2: 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: 2.63 Å3/Da / Density % sol: 53.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 60% Tacsimate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2009 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 85809 / Num. obs: 85799 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.2→2.22 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 3.07 / Num. unique all: 2107 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.549 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.943 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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