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- PDB-4c5a: The X-ray crystal structures of D-alanyl-D-alanine ligase in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c5a | ||||||
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Title | The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
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 | ![]() | 250.4 KB | Display | ![]() |
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PDB format | ![]() | 200.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c5bC ![]() 4c5cC ![]() 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 / Protein/peptide , 2 types, 3 molecules ABC
#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, ![]() #2: Protein/peptide | | ![]() Mass: 940.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 357 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/DS0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DS0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | ![]() #7: 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![]() |
Reflection | Resolution: 1.65→49 Å / Num. obs: 70170 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1IOW Resolution: 1.65→48.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.887 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / 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: 30.664 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→48.76 Å
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Refine LS restraints |
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