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Yorodumi- PDB-8e62: STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8.0E+62 | ||||||
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Title | STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid | ||||||
Components | UDP-N-acetylglucosamine acyltransferase | ||||||
Keywords | TRANSFERASE / N-acetyltransferase / 2 / 3-diacetamido-2 / 3-dideoxy-D-glucuronic acid / Psychrobacter cryohalolentis | ||||||
Function / homology | acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / lipid biosynthetic process / Trimeric LpxA-like superfamily / COENZYME A / Chem-MJZ / UDP-N-acetylglucosamine acyltransferase Function and homology information | ||||||
Biological species | Psychrobacter cryohalolentis K5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hofmeister, D.L. / Bockhaus, N.J. / Seltzner, C.A. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2023 Title: Investigation of the enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid in Psychrobacter cryohalolentis K5 T. Authors: Hofmeister, D.L. / Seltzner, C.A. / Bockhaus, N.J. / 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 | 8e62.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e62.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 8e62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e62_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8e62_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8e62_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 8e62_validation.cif.gz | 67.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/8e62 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/8e62 | HTTPS FTP |
-Related structure data
Related structure data | 8e75C 8e77C 5demS S: Starting model for refinement 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
#1: Protein | Mass: 20516.600 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria) Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0615 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD55 #2: Chemical | #3: Chemical | ChemComp-COA / #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.41 Å3/Da / Density % sol: 48.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein incubated with: 5 mM CoA and 5 mM UDP-GlcNAc3NA. Precipitant: 16 - 20% PEG-3350, 2% 2-methyl-2,4-pentanediol, and 100 mM MES (pH 6.0) |
-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 18, 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: 1.8→50 Å / Num. obs: 102909 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.079 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.3 / Num. unique obs: 5043 / Rsym value: 0.226 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dem Resolution: 1.8→48.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.297 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 114.05 Å2 / Biso mean: 22.1 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: final / Resolution: 1.8→48.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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