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Yorodumi- PDB-4e6t: Structure of LpxA from Acinetobacter baumannii at 1.8A resolution... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e6t | ||||||
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Title | Structure of LpxA from Acinetobacter baumannii at 1.8A resolution (P212121 form) | ||||||
Components | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
Keywords | TRANSFERASE / lipopolysaccharide synthesis | ||||||
Function / homology | Function and homology information Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Badger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii. Authors: Badger, J. / Chie-Leon, B. / Logan, C. / Sridhar, V. / Sankaran, B. / Zwart, P.H. / Nienaber, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e6t.cif.gz | 169.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e6t.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 4e6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e6t_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 4e6t_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 4e6t_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 4e6t_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e6t ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e6t | HTTPS FTP |
-Related structure data
Related structure data | 4e6uC 2qiaS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 31771.938 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: lpxA, ABTW07_2294 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) References: UniProt: F0QHB3, UniProt: A0A7U4DSW1*PLUS, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase #2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2ul of 15mg/ml protein, 2ul of 0.2M Ammonium citrate tribasic, 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.6 Å / Num. all: 72800 / Num. obs: 72800 / % possible obs: 97.2 % / Observed criterion σ(I): -4 / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3 / Num. unique all: 9257 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QIA Resolution: 1.8→47.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.568 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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