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Yorodumi- PDB-6knl: Uridine and triphosphate-bound UGPase from acinetobacter baumannii -
+Open data
-Basic information
Entry | Database: PDB / ID: 6knl | ||||||
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Title | Uridine and triphosphate-bound UGPase from acinetobacter baumannii | ||||||
Components | UTP--glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / UGPase / Rossman fold | ||||||
Function / homology | Function and homology information UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Lee, J.H. / Kang, L.W. | ||||||
Citation | Journal: To be published Title: Uridine and triphosphate-bound UGPase from acinetobacter baumannii Authors: Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6knl.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6knl.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 6knl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/6knl ftp://data.pdbj.org/pub/pdb/validation_reports/kn/6knl | HTTPS FTP |
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-Related structure data
Related structure data | 5j49S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31665.459 Da / Num. of mol.: 2 / Mutation: Q286L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: galU, B9X91_19205, CBI29_00108, CSB70_3798, DVA79_14980 Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: X2KZJ9, UTP-glucose-1-phosphate uridylyltransferase |
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-Non-polymers , 5 types, 39 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 3.05 Å3/Da / Density % sol: 59.69 % / Mosaicity: 0.433 ° |
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Crystal grow | Temperature: 287 K / Method: evaporation / pH: 7.5 Details: 1.5M Ammonium citrate, 0.1M BIS-TRIS pH 6.13 and 0.1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→50 Å / Num. obs: 34574 / % possible obs: 99.6 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.034 / Rrim(I) all: 0.147 / Χ2: 0.642 / Net I/σ(I): 3.7 / Num. measured all: 490694 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J49 Resolution: 2.32→49.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.1853 / FOM work R set: 0.7646 / SU B: 10.826 / SU ML: 0.241 / SU R Cruickshank DPI: 0.2891 / SU Rfree: 0.2444 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.244 / 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: 153.17 Å2 / Biso mean: 39.856 Å2 / Biso min: 20.57 Å2
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Refinement step | Cycle: final / Resolution: 2.32→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.377 Å / Rfactor Rfree error: 0
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