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Yorodumi- PDB-3wdm: Crystal structure of 4-phosphopantoate-beta-alanine ligase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wdm | ||||||
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Title | Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis | ||||||
Components | 4-phosphopantoate--beta-alanine ligase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information 4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Kishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Authors: Kishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdm.cif.gz | 209.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdm.ent.gz | 166.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wdm_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3wdm_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3wdm_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 3wdm_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdm ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdm | HTTPS FTP |
-Related structure data
-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: 29891.600 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1686 / Production host: Escherichia coli (E. coli) References: UniProt: Q5JIZ8, 4-phosphopantoate-beta-alanine ligase #2: Chemical | ChemComp-ADN / #3: 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: 2.13 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 18-20% PEG 3350, 200mM ammonium acetate, 100mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2012 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 66956 / Num. obs: 66956 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→35.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2303449.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.2496 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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