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- PDB-1kgq: Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase... -

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Basic information

Entry
Database: PDB / ID: 1kgq
TitleCrystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with L-2-aminopimelate and Succinamide-CoA
Components2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
KeywordsTRANSFERASE / 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 / L-lysine biosynthetic process via diaminopimelate / nucleotidyltransferase activity / cytoplasm
Similarity search - Function
Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain / Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family / Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat ...Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain / Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family / Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2S)-2-aminoheptanedioic acid / SUCCINAMIDE-COA / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeaman, T.W. / Vogel, K.W. / Drueckhammer, D.G. / Blanchard, J.S. / Roderick, S.L.
CitationJournal: 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
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 1, 2016Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9453
Polymers29,9191
Non-polymers1,0262
Water1,53185
1
A: 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
hetero molecules

A: 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
hetero molecules

A: 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8349
Polymers89,7573
Non-polymers3,0776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area19150 Å2
ΔGint-69 kcal/mol
Surface area26360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.840, 95.840, 72.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe 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

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Components

#1: Protein 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE / TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE / THP SUCCINYLTRANSFERASE / TETRAHYDROPICOLINATE SUCCINYLASE


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
#2: Chemical ChemComp-NPI / (2S)-2-aminoheptanedioic acid / L-2-AMINOPIMELIC ACID


Type: L-peptide linking / Mass: 175.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO4
#3: Chemical ChemComp-SCO / SUCCINAMIDE-COA


Mass: 850.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H41N8O19P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
220 mMHEPES1droppH7.5
312 %PEG40001reservoir
4200 mMammonium sulfate1reservoir
5100 mMMES1reservoirpH6.2
62.5 mMCoA1reservoir
716 mM2-aminopimelate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Apr 26, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 16693 / Num. obs: 16693 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.217 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 3.5 % / Num. measured all: 59293 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
TNTrefinement
X-GENdata reduction
XDSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→99 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: TNT
RfactorNum. reflectionSelection details
Rfree0.25 868 RANDOM
Rwork0.174 --
all0.179 16693 -
obs0.179 16479 -
Refinement stepCycle: LAST / Resolution: 2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 67 85 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg2.2
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / Rfactor Rwork: 0.27 / Rfactor obs: 0.27

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