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Yorodumi- PDB-1kgt: Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kgt | ||||||
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Title | Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA | ||||||
Components | 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / LEFT-HANDED PARALLEL BETA HELIX | ||||||
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: 2.3 Å | ||||||
Authors | Beaman, T.W. / Vogel, K.W. / Drueckhammer, D.G. / Blanchard, J.S. / Roderick, S.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase. Authors: Beaman, T.W. / Vogel, K.W. / Drueckhammer, D.G. / 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 | 1kgt.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kgt.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 1kgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kgt_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 1kgt_full_validation.pdf.gz | 464.2 KB | Display | |
Data in XML | 1kgt_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1kgt_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kgt ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kgt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y, x-y, z and -x+y, 1-x, z. |
-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) / Gene: dapD / Plasmid: pET3a / Species (production host): Escherichia coli / 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-PML / |
#3: Chemical | ChemComp-SCA / |
#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: 2.18 Å3/Da / Density % sol: 43.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 4000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Binder, D.A., (1996) Proteins, 26, 115. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Apr 2, 1999 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 11389 / Num. obs: 11389 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.3→2.5 Å / Rmerge(I) obs: 0.339 / % possible all: 99.9 |
Reflection | *PLUS Redundancy: 4.3 % / Num. measured all: 47749 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→99 Å / σ(F): 2 / Stereochemistry target values: TNT
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Refinement step | Cycle: LAST / Resolution: 2.3→99 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.171 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.171 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.35 / Rfactor obs: 0.35 |