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- PDB-6plj: A nucleotidyl transferase from Methanothermobacter thermautotropt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6plj | ||||||
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Title | A nucleotidyl transferase from Methanothermobacter thermautotroptrophicus (Mth528) | ||||||
![]() | nucleotidyl transferase | ||||||
![]() | TRANSFERASE / Cell wall synthesis / pseudomurein / Methanothermobacter | ||||||
Function / homology | MobA-like NTP transferase / MobA-like NTP transferase domain / Nucleotide-diphospho-sugar transferases / NTP_transf_3 domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Carbone, V. / Schofield, L. / Sutherland-Smith, A. / Ronimus, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A nucleotidyl transferase from Methanothermobacter thermautotroptrophicus (Mth528) Authors: Carbone, V. / Schofield, L. / Sutherland-Smith, A. / Ronimus, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hv9S 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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Unit cell |
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Components
#1: Protein | Mass: 25621.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_528 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.0 M Ammonium sulfate, 0.1 M Bis-Tris, 0.1 M Potassium sodium tartrate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 21, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.59→46.79 Å / Num. obs: 30884 / % possible obs: 99.8 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.7 / Num. measured all: 446457 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.564
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1hv9 Resolution: 1.59→46.79 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.467 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.13 Å2 / Biso mean: 16.827 Å2 / Biso min: 8.37 Å2
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Refinement step | Cycle: final / Resolution: 1.59→46.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.592→1.633 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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