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Yorodumi- PDB-4m99: Acetyltransferase domain of PglB from Neisseria gonorrhoeae FA109... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m99 | ||||||
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Title | Acetyltransferase domain of PglB from Neisseria gonorrhoeae FA1090 in complex with acetyl coenzyme A | ||||||
Components | Pilin glycosylation protein | ||||||
Keywords | TRANSFERASE / left-handed beta-helix / rossmann fold / acetyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Morrison, M.J. / Imperiali, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine. Authors: Morrison, M.J. / Imperiali, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m99.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m99.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 4m99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m99_validation.pdf.gz | 1019.6 KB | Display | wwPDB validaton report |
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Full document | 4m99_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4m99_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4m99_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m99 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m99 | HTTPS FTP |
-Related structure data
Related structure data | 4m98C 4m9cC 3bswS 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: 21032.938 Da / Num. of mol.: 3 / Fragment: unp residues 197-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: NGO0085 / Plasmid: pET-30b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS RIL / References: UniProt: Q5FAE1 #2: Chemical | #3: Chemical | ChemComp-NA / | #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: 3.29 Å3/Da / Density % sol: 62.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M BIS-TRIS , 3.0 M NaCl, 10 mM AcCoA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.978 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→86.955 Å / Num. all: 26704 / Num. obs: 26704 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 23.2 % / Biso Wilson estimate: 57.65 Å2 / Rsym value: 0.105 / Net I/σ(I): 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BSW Resolution: 2.6→64.181 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.32 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.87 Å2 / Biso mean: 52.9819 Å2 / Biso min: 29.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→64.181 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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