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- PDB-5e3p: Crystal structure of DapD from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5e3p
TitleCrystal structure of DapD 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

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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)32,2003
Polymers31,9101
Non-polymers2902
Water1,51384
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)96,6009
Polymers95,7303
Non-polymers8716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11240 Å2
ΔGint-27 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.001, 91.001, 156.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 200, Li2SO4

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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: Dec 23, 2014
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: 2.01→78.81 Å / Num. obs: 24585 / % possible obs: 97.6 % / Redundancy: 14.3 % / Net I/σ(I): 9.68

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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: 3FSX

3fsx


Resolution: 2.01→78.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.804 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIPOSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1265 4.9 %RANDOM
Rwork0.1765 ---
obs0.1785 24585 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.86 Å2 / Biso mean: 33.703 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2.01→78.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 18 84 2191
Biso mean--56.37 43.49 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192140
X-RAY DIFFRACTIONr_bond_other_d0.0020.022036
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9592910
X-RAY DIFFRACTIONr_angle_other_deg1.05434660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.185283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95923.09584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22515323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1731517
X-RAY DIFFRACTIONr_chiral_restr0.1240.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022452
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
X-RAY DIFFRACTIONr_mcbond_it3.1393.1631135
X-RAY DIFFRACTIONr_mcbond_other3.1273.1591134
X-RAY DIFFRACTIONr_mcangle_it4.4014.7251417
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 77 -
Rwork0.205 1678 -
all-1755 -
obs--91.64 %

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