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Yorodumi- PDB-8vr6: crystal structure of the Pcryo_0619 N-acetryltransferase from Psy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vr6 | ||||||
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Title | crystal structure of the Pcryo_0619 N-acetryltransferase from Psychrobacter cryohalolentis K5 in the presence of CoA-disulfide | ||||||
Components | Acetyltransferase, putative | ||||||
Keywords | TRANSFERASE / psychrobacter / n-acetyltransferase / 2 / 3 / 4-triacetoamido-2 / 4-trideoxy-l-arabinose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Psychrobacter cryohalolentis K5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Dunsirn, M.M. / Bockhaus, N.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5 Authors: Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vr6.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vr6.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 8vr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vr6 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vr6 | HTTPS FTP |
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-Related structure data
Related structure data | 8vr2C 8vr3C 8vr5C 8vr7C 8vrmC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19598.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria) Gene: Pcryo_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD51 |
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#2: Chemical | ChemComp-5NG / [[( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein incubated with 2 mM coenzyme A. Precipitant: 23-26% pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES (pH 6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 19728 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.079 / Net I/σ(I): 52 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.9 % / Num. unique obs: 973 / R split: 2.1 / Rsym value: 0.47 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→40.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.305 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / 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: 52.283 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→40.62 Å
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Refine LS restraints |
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