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Yorodumi- PDB-2tdt: COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tdt | ||||||
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Title | COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINOPIMELATE AND COENZYME A | ||||||
Components | TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE | ||||||
Keywords | ACYLTRANSFERASE / LYSINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 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 | Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Beaman, T.W. / Blanchard, J.S. / Roderick, S.L. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Authors: Beaman, T.W. / Blanchard, J.S. / Roderick, S.L. #1: Journal: Biochemistry / Year: 1997 Title: Three-Dimensional Structure of Tetrahydrodipicolinate N-Succinyltransferase Authors: Beaman, T.W. / Binder, D.A. / Blanchard, J.S. / Roderick, S.L. #2: Journal: Proteins / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tdt.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tdt.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 2tdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tdt_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
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Full document | 2tdt_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 2tdt_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 2tdt_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/2tdt ftp://data.pdbj.org/pub/pdb/validation_reports/td/2tdt | HTTPS FTP |
-Related structure data
Related structure data | 3tdtC 1tdtS 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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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.) Mycobacterium bovis (bacteria) / Cell line: BL21 / Gene: DAPD / Plasmid: PET3A / Species (production host): Escherichia coli / Gene (production host): DAPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |