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Yorodumi- PDB-4xpk: The crystal structure of Campylobacter jejuni N-acetyltransferase PseH -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xpk | ||||||
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Title | The crystal structure of Campylobacter jejuni N-acetyltransferase PseH | ||||||
Components | N-Acetyltransferase, PseH | ||||||
Keywords | TRANSFERASE / Campylobacter jejuni / PseH / bacterial glycosylation / N-acetyltransferase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni PT14 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Song, W.S. / Nam, M.S. / Namgung, B. / Yoon, S.I. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Structural analysis of PseH, the Campylobacter jejuni N-acetyltransferase involved in bacterial O-linked glycosylation. Authors: Song, W.S. / Nam, M.S. / Namgung, B. / Yoon, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xpk.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xpk.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xpk_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 4xpk_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 4xpk_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 4xpk_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xpk ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xpk | HTTPS FTP |
-Related structure data
Related structure data | 4xplC 4jjxS 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: 19379.373 Da / Num. of mol.: 1 Mutation: M1L, N107S, D120S, R122H, H144Y, I145V, C146Y, D151N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni PT14 (Campylobacter) Gene: A911_06385 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0HK73, UniProt: A0A0J9X276*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 22-24% PEG MME 550, 4mM reduced glutathione, 4mM oxidized glutathione, 0.1M phosphate-citrate PH range: 4.4-4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen cryo-stream | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→30 Å / Num. obs: 14574 / % possible obs: 98.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 3.104 / Net I/av σ(I): 43 / Net I/σ(I): 23.2 / Num. measured all: 79770 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JJX Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 72.01 Å2 / Biso mean: 32.9 Å2 / Biso min: 14.51 Å2
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Refinement step | Cycle: final / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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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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