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Yorodumi- PDB-4c5b: The X-ray crystal structure of D-alanyl-D-alanine ligase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c5b | ||||||
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Title | The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ATP and D-ala-D-ala | ||||||
Components | D-ALANINE--D-ALANINE LIGASE | ||||||
Keywords | LIGASE / DDLB | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / protein homodimerization activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Batson, S. / Majce, V. / Lloyd, A.J. / Rea, D. / Fishwick, C.W.G. / Simmons, K.J. / Fulop, V. / Roper, D.I. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Authors: Batson, S. / de Chiara, C. / Majce, V. / Lloyd, A.J. / Gobec, S. / Rea, D. / Fulop, V. / Thoroughgood, C.W. / Simmons, K.J. / Dowson, C.G. / Fishwick, C.W.G. / de Carvalho, L.P.S. / Roper, D.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c5b.cif.gz | 260.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c5b.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5b ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5b | HTTPS FTP |
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-Related structure data
Related structure data | 4c5aC 4c5cC 1iowS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35840.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR-ROSETTA References: UniProt: C4ZRI7, UniProt: P07862*PLUS, D-alanine-D-alanine ligase |
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-Non-polymers , 7 types, 783 molecules
#2: Chemical | #3: Chemical | ChemComp-DAL / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-IMD / | #8: 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: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48 Å / Num. obs: 91443 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IOW Resolution: 1.5→47.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.445 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.076 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.99 Å
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Refine LS restraints |
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