+Open data
-Basic information
Entry | Database: PDB / ID: 2xja | ||||||
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Title | Structure of MurE from M.tuberculosis with dipeptide and ADP | ||||||
Components | UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE | ||||||
Keywords | LIGASE / PEPTIDOGLYCAN / PEPTIDASE LIGASE | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane ...UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Basavannacharya, C. / Moody, P.R. / Bhakta, S. / Keep, N. | ||||||
Citation | Journal: Protein Cell / Year: 2010 Title: Essential Residues for the Enzyme Activity of ATP-Dependent Mure Ligase from Mycobacterium Tuberculosis. Authors: Basavannacharya, C. / Moody, P.R. / Munshi, T. / Cronin, N. / Keep, N.H. / Bhakta, S. #1: Journal: Tuberculosis (Edinb) / Year: 2010 Title: ATP-Dependent Mure Ligase in Mycobacterium Tuberculosis: Biochemical and Structural Characterisation. Authors: Basavannacharya, C. / Robertson, G. / Munshi, T. / Keep, N.H. / Bhakta, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xja.cif.gz | 746.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xja.ent.gz | 615.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xja_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 2xja_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 2xja_validation.xml.gz | 79.4 KB | Display | |
Data in CIF | 2xja_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xja ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xja | HTTPS FTP |
-Related structure data
Related structure data | 2wtzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 55454.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/PLYSS References: UniProt: P65477, UniProt: P9WJL3*PLUS, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-UAG / #5: 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: 1.96 Å3/Da / Density % sol: 37.4 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.35 M MGCL2, 0.1 M TRIS PH 8.5, 16% PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3→74.8 Å / Num. obs: 31925 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WTZ Resolution: 3→76.3 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.867 / SU B: 46.79 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 61.12 Å2
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Refinement step | Cycle: LAST / Resolution: 3→76.3 Å
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Refine LS restraints |
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