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Yorodumi- PDB-7l82: x-ray structure of the psychrobacter cryohalolentis Pcryo_0637 N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l82 | ||||||
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Title | x-ray structure of the psychrobacter cryohalolentis Pcryo_0637 N-acetyltransferase in the presene of its reaction tetrahedral intermediate | ||||||
Components | Putative acetyl transferase protein | ||||||
Keywords | TRANSFERASE / beta helix / reaction intermediate / N-acetyltransferase | ||||||
Function / homology | Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Trimeric LpxA-like superfamily / transferase activity / nucleotide binding / Chem-XQD / Acetyl transferase protein Function and homology information | ||||||
Biological species | Psychrobacter cryohalolentis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Linehan, M.P. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar. Authors: Linehan, M.P. / 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 | 7l82.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l82.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7l82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l82_validation.pdf.gz | 722.3 KB | Display | wwPDB validaton report |
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Full document | 7l82_full_validation.pdf.gz | 724.3 KB | Display | |
Data in XML | 7l82_validation.xml.gz | 14 KB | Display | |
Data in CIF | 7l82_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/7l82 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/7l82 | HTTPS FTP |
-Related structure data
Related structure data | 7l7xC 7l7ySC 7l7zC 7l81C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23680.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5) (bacteria) Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QD33 | ||||
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#2: Chemical | ChemComp-XQD / [( | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-MPD / ( #5: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 23-26% MPD, 100 mM HEPES crystals incubated with 5 mM acetyl-coenzyme A and 5 mM UDP-2-acetamido-4-amino-2,4,3-trideoxy-D-glucose |
-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: Apr 3, 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: 1.399→50 Å / Num. obs: 45470 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.049 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8481 / Rsym value: 0.38 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7l7y Resolution: 1.4→28.699 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.029 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.056 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→28.699 Å
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Refine LS restraints |
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LS refinement shell |
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