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Yorodumi- PDB-2bi8: udp-galactopyranose mutase from Klebsiella pneumoniae with reduced FAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bi8 | ||||||
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Title | udp-galactopyranose mutase from Klebsiella pneumoniae with reduced FAD | ||||||
Components | UDP-GALACTOPYRANOSE MUTASE | ||||||
Keywords | ISOMERASE / FAD / FLAVOPROTEIN / LIPOPOLYSACCHARIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / O antigen biosynthetic process Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Beis, K. / Srikannathasan, V. / Naismith, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of Mycobacteria Tuberculosis and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the Oxidised State and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the (Active) Reduced State. Authors: Beis, K. / Srikannathasan, V. / Liu, H. / Fullerton, S.W.B. / Bamford, V.A. / Sanders, D.A.R. / Whitfield, C. / McNeil, M.R. / Naismith, J.H. #1: Journal: Nat.Struct.Biol. / Year: 2001 Title: Udp-Galactopyranose Mutase Has a Novel Structure and Mechanism Authors: Sanders, D.A. / Staines, A.G. / McMahon, S.A. / McNeil, M.R. / Whitfield, C. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bi8.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bi8.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2bi8 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bi8 | HTTPS FTP |
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-Related structure data
Related structure data | 1v0jC 1wamC 2bi7C 1i8tS C: citing same article (ref.) 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
#1: Protein | Mass: 44512.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q48485, UDP-galactopyranose mutase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Compound details | FUNCTION: INVOLVED IN THE CONVERSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 6.5 Details: 0.1M BIS-TRIS PH6.5,50MM CACL2, 30% PEG550, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→27.12 Å / Num. obs: 18331 / % possible obs: 99.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I8T Resolution: 2.35→27.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→27.12 Å
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Refine LS restraints |
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