+Open data
-Basic information
Entry | Database: PDB / ID: 6knj | ||||||
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Title | UTP-bound UGPase from acinetobacter baumannii | ||||||
Components | (UTP--glucose-1-phosphate ...) x 2 | ||||||
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: 3.2 Å | ||||||
Authors | Lee, J.H. / Kang, L.W. | ||||||
Citation | Journal: To be published Title: UTP-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 | 6knj.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6knj.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 6knj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6knj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6knj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6knj_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 6knj_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/6knj ftp://data.pdbj.org/pub/pdb/validation_reports/kn/6knj | HTTPS FTP |
-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
-UTP--glucose-1-phosphate ... , 2 types, 2 molecules AB
#1: Protein | Mass: 31697.459 Da / Num. of mol.: 1 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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#2: Protein | Mass: 31665.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: galU, B9X91_19205, CBI29_00108, CSB70_3798, DVA79_14980 Production host: Escherichia coli (E. coli) References: UniProt: X2KZJ9, UTP-glucose-1-phosphate uridylyltransferase |
-Non-polymers , 4 types, 6 molecules
#3: Chemical | ChemComp-SO4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-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: 3.04 Å3/Da / Density % sol: 59.52 % |
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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: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 32126 / % possible obs: 97.4 % / Redundancy: 6.7 % / Rpim(I) all: 0.05 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.2→3.283 Å / Rmerge(I) obs: 0.459 / Num. unique obs: 13108 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J49 Resolution: 3.2→49.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / SU B: 70.4 / SU ML: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.561 Details: U VALUES : WITH TLS ADDED 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.14 Å2 / Biso mean: 51.955 Å2 / Biso min: 26.98 Å2
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Refinement step | Cycle: final / Resolution: 3.2→49.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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