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Yorodumi- PDB-3zl8: CRYSTAL STRUCTURE OF MURF LIGASE FROM THERMOTOGA MARITIMA IN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zl8 | ||||||
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Title | CRYSTAL STRUCTURE OF MURF LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP | ||||||
Components | UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE | ||||||
Keywords | LIGASE / PEPTIDOGLYCAN SYNTHESIS / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / ATP-BINDING / CELL DIVISION | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Favini-Stabile, S. / Contreras-Martel, C. / Thielens, N. / Dessen, A. | ||||||
Citation | Journal: Environ.Microbiol. / Year: 2013 Title: Mreb and Murg as Scaffolds for the Cytoplasmic Steps of Peptidoglycan Biosynthesis Authors: Favini-Stabile, S. / Contreras-Martel, C. / Thielens, N. / Dessen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zl8.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zl8.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zl8_validation.pdf.gz | 836.2 KB | Display | wwPDB validaton report |
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Full document | 3zl8_full_validation.pdf.gz | 840.5 KB | Display | |
Data in XML | 3zl8_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 3zl8_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zl8 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zl8 | HTTPS FTP |
-Related 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: 49251.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q9WY78, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.02 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1M SODIUM ACETATE PH 5.5, 45-49%(V/V) 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.54 Å / Num. obs: 50746 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 28.741 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.65→46.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.755 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 25.235 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→46.54 Å
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Refine LS restraints |
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