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Yorodumi- PDB-3zm5: CRYSTAL STRUCTURE OF MURF LIGASE IN COMPLEX WITH CYANOTHIOPHENE I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zm5 | ||||||
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Title | CRYSTAL STRUCTURE OF MURF LIGASE IN COMPLEX WITH CYANOTHIOPHENE INHIBITOR | ||||||
Components | UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE | ||||||
Keywords | LIGASE / PEPTIDOGLYCAN SYNTHESIS / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / CELL DIVISON / NUCLEOTIDE-BINDING / ATP-BINDING | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / 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 | STREPTOCOCCUS PNEUMONIAE R6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Hrast, M. / Turk, S. / Sosic, I. / Knez, D. / Randall, C.P. / Barreteau, H. / Contreras-Martel, C. / Dessen, A. / ONeill, A.J. / Mengin-Lecreulx, D. ...Hrast, M. / Turk, S. / Sosic, I. / Knez, D. / Randall, C.P. / Barreteau, H. / Contreras-Martel, C. / Dessen, A. / ONeill, A.J. / Mengin-Lecreulx, D. / Blanot, D. / Gobec, S. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2013 Title: Structure-Activity Relationships of New Cyanothiophene Inhibitors of the Essential Peptidoglycan Biosynthesis Enzyme Murf. Authors: Hrast, M. / Turk, S. / Sosic, I. / Knez, D. / Randall, C.P. / Barreteau, H. / Contreras-Martel, C. / Dessen, A. / O'Neill, A.J. / Mengin-Lecreulx, D. / Blanot, D. / Gobec, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zm5.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zm5.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zm5_validation.pdf.gz | 669.2 KB | Display | wwPDB validaton report |
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Full document | 3zm5_full_validation.pdf.gz | 681.7 KB | Display | |
Data in XML | 3zm5_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 3zm5_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zm5 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zm5 | HTTPS FTP |
-Related structure data
Related structure data | 3zm6C 2am1S 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: 51630.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE R6 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: Q8DNV6, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase |
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#2: Chemical | ChemComp-IGM / |
#3: 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: 3.26 Å3/Da / Density % sol: 62.28 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 0.1 M TRIS SODIUM CITRATE PH 5.6, 0.2 M K/NA-TARTRATE AND 2.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→43.42 Å / Num. obs: 13459 / % possible obs: 89.8 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 76.16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 46 |
Reflection shell | Resolution: 2.94→3.11 Å / Redundancy: 9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 9 / % possible all: 85.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AM1 Resolution: 2.94→43.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 48.036 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.748 Å2
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Refinement step | Cycle: LAST / Resolution: 2.94→43.42 Å
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Refine LS restraints |
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