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Yorodumi- PDB-8vr7: crystal structure of the Pcryo_0619 N-acetyltransferase from Psyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vr7 | ||||||
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Title | crystal structure of the Pcryo_0619 N-acetyltransferase from Psychrobacter cryohalolentis K5 int he presence of acetyl coenzyme A | ||||||
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 / MOLECULAR REPLACEMENT / 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 | 8vr7.cif.gz | 236 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vr7.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/8vr7 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/8vr7 | HTTPS FTP |
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-Related structure data
Related structure data | 8vr2C 8vr3C 8vr5C 8vr6C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 19598.547 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria) Strain: Pcryo_0619 / Gene: Pcryo_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD51 |
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-Non-polymers , 6 types, 682 molecules
#2: Chemical | ChemComp-ACO / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EP1 / | #6: Chemical | ChemComp-PAP / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein incubated with 3 mM acetyl-CoA. Precipitant: 8-12% PEG 8000 and 100 mM homopipes (pH 5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Nov 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 89307 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rsym value: 0.084 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12536 / Rsym value: 0.4 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.632 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.153 / 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: 18.034 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.69 Å
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