+Open data
-Basic information
Entry | Database: PDB / ID: 1v0j | ||||||
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Title | Udp-galactopyranose mutase from Mycobacterium tuberculosis | ||||||
Components | UDP-GALACTOPYRANOSE MUTASE | ||||||
Keywords | ISOMERASE / MUTASE / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information Actinobacterium-type cell wall biogenesis / UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / capsule polysaccharide biosynthetic process / peptidoglycan-based cell wall / cell wall organization / flavin adenine dinucleotide binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Beis, K. / 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. / Bamford, V.A. / Sanders, D.A. / 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.R. / 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 | 1v0j.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v0j.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 1v0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/1v0j ftp://data.pdbj.org/pub/pdb/validation_reports/v0/1v0j | HTTPS FTP |
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-Related structure data
Related structure data | 1wamC 2bi7C 2bi8C 1i8tS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 45868.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: FAD COFACTOR AND BICINE / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET29B / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O06934, UniProt: P9WIQ1*PLUS, UDP-galactopyranose mutase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-BCN / | #4: 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: 4 Å3/Da / Density % sol: 69.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M BICINE PH9.0, 1.6M AMMONIUM SULPHATE, 277K, pH 9.00 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→24.5 Å / Num. obs: 1188969 / % possible obs: 89 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.1 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I8T Resolution: 2.25→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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 mean: 41.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→15 Å
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Refine LS restraints |
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