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Yorodumi- PDB-2zdh: Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zdh | ||||||
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Title | Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8 | ||||||
Components | D-alanine--D-alanine ligase | ||||||
Keywords | LIGASE / D-Alanine-D-Alanine Ligase / Peptidoglycan Biosynthesis / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Kitamuta, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8 Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zdh.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zdh.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zdh ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zdh | HTTPS FTP |
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-Related structure data
Related structure data | 2zdgS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34699.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHZ3, D-alanine-D-alanine ligase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / #4: Chemical | #5: 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: 2.61 Å3/Da / Density % sol: 52.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 12% PEG3350, 0.1M Bis-Tris, 0.1M Mg Formate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2007 Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium. |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 115364 / Num. obs: 114964 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.078 / Net I/σ(I): 23.24 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 4.09 / Num. unique all: 11187 / Rsym value: 0.317 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZDG Resolution: 1.9→47.9 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 70485.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.8588 Å2 / ksol: 0.354107 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→47.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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