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- PDB-2tdt: COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2tdt | ||||||
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Title | COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINOPIMELATE AND COENZYME A | ||||||
![]() | TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE | ||||||
![]() | ACYLTRANSFERASE / LYSINE BIOSYNTHESIS | ||||||
Function / homology | ![]() 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotidyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Beaman, T.W. / Blanchard, J.S. / Roderick, S.L. | ||||||
![]() | ![]() Title: The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Authors: Beaman, T.W. / Blanchard, J.S. / Roderick, S.L. #1: ![]() Title: Three-Dimensional Structure of Tetrahydrodipicolinate N-Succinyltransferase Authors: Beaman, T.W. / Binder, D.A. / Blanchard, J.S. / Roderick, S.L. #2: ![]() Title: Crystallization and Preliminary Crystallographic Analysis of Tetrahydrodipicolinate-N-Succinyltransferase Authors: Binder, D.A. / Blanchard, J.S. / Roderick, S.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.9 KB | Display | ![]() |
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PDB format | ![]() | 49.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tdtC ![]() 1tdtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29918.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P56220, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-NPI / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: 10-13 % (W/V) POLYETHYLENE GLYCOL 4000 94 MM MES, PH 6.4 94 MM AMMONIUM SULFATE 4.7 (V/V) 2-PROPANOL 16 MM (D,L)-2-AMINOPIMELATE 2.5 MM COENZYME A | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 44276 / % possible obs: 98.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.215 / % possible all: 98.1 |
Reflection shell | *PLUS % possible obs: 92.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TDT Resolution: 2→99 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 205 Å2 / ksol: 0.61 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→99 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / Rfactor obs: 0.26 |