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- PDB-4c5c: The X-ray crystal structure of D-alanyl-D-alanine ligase in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c5c | ||||||
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Title | The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala | ||||||
![]() | D-ALANINE--D-ALANINE LIGASE | ||||||
![]() | LIGASE / DDLB | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batson, S. / Majce, V. / Lloyd, A.J. / Rea, D. / Fishwick, C.W.G. / Simmons, K.J. / Fulop, V. / Roper, D.I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.7 KB | Display | ![]() |
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PDB format | ![]() | 204.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c5aC ![]() 4c5bC ![]() 1iowS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: C4ZRI7, UniProt: P07862*PLUS, D-alanine-D-alanine ligase |
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-Non-polymers , 5 types, 667 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/DAL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DAL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-DAL / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: 1.4→49 Å / Num. obs: 106127 / % possible obs: 97.1 % / Observed criterion σ(I): 2.1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IOW Resolution: 1.4→48.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.053 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / 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: 16.101 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.9 Å
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Refine LS restraints |
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