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- PDB-1tdt: THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLT... -

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Basic information

Entry
Database: PDB / ID: 1tdt
TitleTHREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
ComponentsTETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
KeywordsTRANSFERASE / 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 / 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
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MIR - 2 HEAVY ATOM DERIVATIVES / Resolution: 2.2 Å
AuthorsBeaman, 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
DepositionNov 19, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
B: TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
C: TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)84,7473
Polymers84,7473
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-62 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.600, 107.900, 70.700
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1684, 0.50037, -0.84928), (0.73035, 0.64196, 0.2334), (0.66169, -0.58096, -0.47355)-5.89603, -0.43918, -23.76383
2given(-0.1684, 0.73035, 0.66199), (0.50037, 0.64196, -0.58096), (-0.84928, 0.2334, -0.47355)15.05919, -10.57381, -16.15831

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Components

#1: Protein TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE / THDP-SUCCINYLTRANSFERASE / DAPD


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 / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
116 %(w/v)PEG400011
2200 mMammonium sulfate11
3100 mMHEPES11
410 %(v/v)2-propanol11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 38447 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.2→2.3 Å / % possible all: 73
Reflection
*PLUS
Num. measured all: 137056
Reflection shell
*PLUS
% possible obs: 73 %

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Processing

Software
NameClassification
PHASESphasing
TNTrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.23 1921 5 %
Rwork0.17 --
all-38447 -
obs-38447 90 %
Solvent computationBsol: 187.3 Å2 / ksol: 0.679 e/Å3
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 0 215 5995
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00958820.8
X-RAY DIFFRACTIONt_angle_deg1.9779761.3
X-RAY DIFFRACTIONt_dihedral_angle_d24.135150
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0051502
X-RAY DIFFRACTIONt_gen_planes0.018715
X-RAY DIFFRACTIONt_it3.93117643
X-RAY DIFFRACTIONt_nbd0.022610
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
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0052
X-RAY DIFFRACTIONt_plane_restr0.015

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