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Yorodumi- PDB-1tae: Structural rearrangement accompanying NAD+ synthesis within a bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tae | ||||||
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Title | Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal | ||||||
Components | DNA ligase, NAD-dependent | ||||||
Keywords | LIGASE / Nucleotidyl transferase fold | ||||||
Function / homology | Function and homology information DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA replication / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Gajiwala, K.S. / Pinko, C. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. Authors: Gajiwala, K.S. / Pinko, C. #1: Journal: Structure / Year: 1999 Title: Structure of the adenylation domain of an NAD dependent DNA ligase Authors: Singleton, M.R. / Hakansson, K. / Timson, D.J. / Wigley, D.B. #2: Journal: Embo J. / Year: 2000 Title: Crystal structure of NAD dependent DNA ligase: modular architecture and functional implications. Authors: Lee, J.Y. / Chang, C. / Song, H.K. / Moon, J. / Yang, J.K. / K Kim, H. / Kwon, S.T. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tae.cif.gz | 250.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tae.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/1tae ftp://data.pdbj.org/pub/pdb/validation_reports/ta/1tae | HTTPS FTP |
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-Related structure data
Related structure data | 1ta8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38032.688 Da / Num. of mol.: 4 / Fragment: Adenylation domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: ligA / Production host: Escherichia coli (E. coli) References: UniProt: Q837V6, GenBank: 29375318, DNA ligase (NAD+) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #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: 3.13 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Ammonium sulfate, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 2004 / Details: Osmic Confocal Max-Flux Optics |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 51184 / Num. obs: 50300 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.84 % / Biso Wilson estimate: 56.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 4916 / Rsym value: 0.374 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Domain 1b of NMN bound structure of E. faecalis ligase (PDB ID: 1TA8) Resolution: 2.7→24.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 482888.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.2795 Å2 / ksol: 0.369729 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→24.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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