+Open data
-Basic information
Entry | Database: PDB / ID: 6ikz | ||||||
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Title | UDP-glucose pyrophosphorylase from acinetobacter baumanii | ||||||
Components | UTP--glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / UDP-glucose pyrophosphorylase from acinetobacter baumanii | ||||||
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: 2.33 Å | ||||||
Authors | Lee, J.H. / Kang, L.W. | ||||||
Citation | Journal: To be published Title: UTP-bound UGPase from acinetobacter baumanii 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 | 6ikz.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ikz.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ikz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ikz_validation.pdf.gz | 760 KB | Display | wwPDB validaton report |
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Full document | 6ikz_full_validation.pdf.gz | 768.8 KB | Display | |
Data in XML | 6ikz_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 6ikz_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/6ikz ftp://data.pdbj.org/pub/pdb/validation_reports/ik/6ikz | 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
-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, 17 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PPV / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-UTP / | #6: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.19 % / Mosaicity: 0.547 ° |
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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: 2.14→50 Å / Num. obs: 42093 / % possible obs: 97.8 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Χ2: 3.258 / Net I/σ(I): 15 / Num. measured all: 499943 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.33→37.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.946 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.266 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 239.57 Å2 / Biso mean: 56.089 Å2 / Biso min: 31.81 Å2
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Refinement step | Cycle: final / Resolution: 2.33→37.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.331→2.391 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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