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Yorodumi- PDB-6u1e: Thermus thermophilus D-alanine-D-alanine ligase in complex with A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u1e | ||||||
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Title | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, Mg2+ and Rb+ | ||||||
Components | D-alanine--D-alanine ligase | ||||||
Keywords | LIGASE / ATP-grasp domain / ATP binding / metal binding | ||||||
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 / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Pederick, J.L. / Bruning, J.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u1e.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u1e.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 6u1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u1e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6u1e_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6u1e_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 6u1e_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/6u1e ftp://data.pdbj.org/pub/pdb/validation_reports/u1/6u1e | HTTPS FTP |
-Related structure data
Related structure data | 6u1cC 6u1dSC 6u1fC 6u1gC 6u1hC 6u1iC 6u1jC 6u1kC 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: 35788.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: ddl, TTHA1587 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHZ3, D-alanine-D-alanine ligase |
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-Non-polymers , 5 types, 297 molecules
#2: Chemical | ChemComp-DAL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-RB / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.06 Å3/Da / Density % sol: 59.85 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 15-18% PEG 3350, 100mM Bis-Tris pH 6.8, 100mM magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.813 Å | ||||||||||||||||||||||||||||||
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: 0.813 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→47.72 Å / Num. obs: 53055 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.028 / Rrim(I) all: 0.145 / Net I/σ(I): 18.7 / Num. measured all: 1363931 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U1D Resolution: 2.1→38.358 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.26 / 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: 108.94 Å2 / Biso mean: 46.5186 Å2 / Biso min: 27.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→38.358 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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