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- PDB-6u1k: Thermus thermophilus D-alanine-D-alanine ligase in complex with A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u1k | ||||||
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Title | Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate, D-alanine-D-alanine, Mg2+ and K+ | ||||||
![]() | D-alanine--D-alanine ligase | ||||||
![]() | LIGASE / ATP-grasp domain / ATP binding / metal binding | ||||||
Function / homology | ![]() D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pederick, J.L. / Bruning, J.B. | ||||||
![]() | ![]() Title: d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. Authors: Pederick, J.L. / Thompson, A.P. / Bell, S.G. / Bruning, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.9 KB | Display | ![]() |
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PDB format | ![]() | 218.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 54.7 KB | Display | |
Data in CIF | ![]() | 78.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u1cC ![]() 6u1dC ![]() 6u1eC ![]() 6u1fC ![]() 6u1gC ![]() 6u1hC ![]() 6u1iC ![]() 6u1jC ![]() 2zdhS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35788.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: ddl, TTHA1587 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 832 molecules ![](data/chem/img/DAL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DAL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-ADP / #6: Chemical | ChemComp-CO3 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.55 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 15-18% PEG 3350, 100 mM Bis-Tris pH 6.8, 100 mM magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→48.15 Å / Num. obs: 127289 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.074 / Rrim(I) all: 0.139 / Net I/σ(I): 6.2 / Num. measured all: 430702 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZDH Resolution: 1.67→43.575 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.64 Å2 / Biso mean: 23.9075 Å2 / Biso min: 7.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→43.575 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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