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Yorodumi- PDB-1tdt: THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tdt | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE | ||||||
Components | TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / SUCCINYLTRANSFERASE / LYSINE METABOLISM / HEXAPEPTIDE TRANSFERASE / CELL WALL 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR - 2 HEAVY ATOM DERIVATIVES / Resolution: 2.2 Å | ||||||
Authors | Beaman, T.W. / Binder, D.W. / Blanchard, J.S. / Roderick, S.L. | ||||||
Citation | 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. #1: 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 | 1tdt.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tdt.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/1tdt ftp://data.pdbj.org/pub/pdb/validation_reports/td/1tdt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28249.055 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium bovis (bacteria) / Cell line: BL21 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P56220 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 14-19 % (W/V) POLYETHYLENEGLYCOL 4000 200 MM AMMONIUM SULFATE 6-12 % 2-PROPANOL 100 MM HEPES, PH 7.5, | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1996 |
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: 2.2 Å / Num. obs: 38447 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 73 |
Reflection | *PLUS Num. measured all: 137056 |
Reflection shell | *PLUS % possible obs: 73 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR - 2 HEAVY ATOM DERIVATIVES Highest resolution: 2.2 Å / Isotropic thermal model: BCORREL.DAT (WEIGHTS GIVEN ABOVE) / σ(F): 0 / Stereochemistry target values: PROTGEO.DAT
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Solvent computation | Bsol: 187.3 Å2 / ksol: 0.679 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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