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- PDB-5e3r: Crystal structure of DapD in complex with 2-aminopimelate from Co... -

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Basic information

Entry
Database: PDB / ID: 5e3r
TitleCrystal structure of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum
Components2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
KeywordsTRANSFERASE / Corynebacterium glutamicum / L-lysine
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 / magnesium ion binding / cytoplasm
Similarity search - Function
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, actinobacteria / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins ...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, actinobacteria / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminoheptanedioic acid / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: J.Agric.Food Chem. / Year: 2015
Title: Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.
Authors: Sagong, H.Y. / Kim, K.J.
History
DepositionOct 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Sep 9, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_oper_list / struct
Item: _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0852
Polymers31,9101
Non-polymers1751
Water2,522140
1
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2556
Polymers95,7303
Non-polymers5263
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9520 Å2
ΔGint6 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.446, 92.446, 279.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

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Components

#1: Protein 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / Tetrahydrodipicolinate N-succinyltransferase / THP succinyltransferase / Tetrahydropicolinate succinylase


Mass: 31909.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: dapD, Cgl1106, cg1256 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8NRE3, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 200, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 15, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→93.2 Å / Num. obs: 36690 / % possible obs: 97.8 % / Redundancy: 5.1 % / Net I/σ(I): 32.36
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.15 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E3P

5e3p


Resolution: 1.85→93.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.106 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2007 5.2 %RANDOM
Rwork0.1776 ---
obs0.179 36690 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.16 Å2 / Biso mean: 28.762 Å2 / Biso min: 4.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å2-0 Å2
2--0.9 Å2-0 Å2
3----2.92 Å2
Refinement stepCycle: final / Resolution: 1.85→93.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 12 140 2198
Biso mean--53.4 42.28 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192090
X-RAY DIFFRACTIONr_bond_other_d0.0020.021998
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.962843
X-RAY DIFFRACTIONr_angle_other_deg1.11734572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.52623.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78715320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5231517
X-RAY DIFFRACTIONr_chiral_restr0.1540.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02467
X-RAY DIFFRACTIONr_mcbond_it2.9852.6181109
X-RAY DIFFRACTIONr_mcbond_other2.9122.6121107
X-RAY DIFFRACTIONr_mcangle_it3.8363.8961381
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 163 -
Rwork0.238 2647 -
all-2810 -
obs--97.4 %

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