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- PDB-7kly: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kly
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsSaran, S. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME
Authors: Saran, S. / Skovpen, Y. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionNov 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,68388
Polymers204,9676
Non-polymers6,71682
Water17,240957
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50029
Polymers68,3222
Non-polymers2,17727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-12 kcal/mol
Surface area22680 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,74033
Polymers68,3222
Non-polymers2,41831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-12 kcal/mol
Surface area22010 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,44426
Polymers68,3222
Non-polymers2,12124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint15 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.520, 231.490, 201.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5:20 or resid 22:24 or resid...
21(chain B and (resid 5:20 or resid 22:24 or resid...
31(chain C and (resid 5:20 or resid 22:24 or resid...
41(chain D and (resid 5:20 or resid 22:24 or resid...
51(chain E and (resid 5:20 or resid 22:24 or resid...
61(chain F and (resid 5:20 or resid 22:24 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5:20 or resid 22:24 or resid...A5 - 20
121(chain A and (resid 5:20 or resid 22:24 or resid...A22 - 24
131(chain A and (resid 5:20 or resid 22:24 or resid...A26 - 28
141(chain A and (resid 5:20 or resid 22:24 or resid...A30 - 31
151(chain A and (resid 5:20 or resid 22:24 or resid...A37 - 38
161(chain A and (resid 5:20 or resid 22:24 or resid...A40 - 50
171(chain A and (resid 5:20 or resid 22:24 or resid...A52 - 58
181(chain A and (resid 5:20 or resid 22:24 or resid...A60 - 73
191(chain A and (resid 5:20 or resid 22:24 or resid...A3 - 298
1101(chain A and (resid 5:20 or resid 22:24 or resid...A3 - 298
1111(chain A and (resid 5:20 or resid 22:24 or resid...A143 - 159
1121(chain A and (resid 5:20 or resid 22:24 or resid...A162 - 165
1131(chain A and (resid 5:20 or resid 22:24 or resid...A167 - 1838
1141(chain A and (resid 5:20 or resid 22:24 or resid...A220 - 28
1151(chain A and (resid 5:20 or resid 22:24 or resid...A220 - 230
1161(chain A and (resid 5:20 or resid 22:24 or resid...A233 - 23279
1171(chain A and (resid 5:20 or resid 22:24 or resid...A28276
1181(chain A and (resid 5:20 or resid 22:24 or resid...A278 - 279
1191(chain A and (resid 5:20 or resid 22:24 or resid...A282 - 291
1201(chain A and (resid 5:20 or resid 22:24 or resid...A293
1211(chain A and (resid 5:20 or resid 22:24 or resid...A295 - 298
211(chain B and (resid 5:20 or resid 22:24 or resid...B5 - 20
221(chain B and (resid 5:20 or resid 22:24 or resid...B22 - 24
231(chain B and (resid 5:20 or resid 22:24 or resid...B26 - 28
241(chain B and (resid 5:20 or resid 22:24 or resid...B30 - 31
251(chain B and (resid 5:20 or resid 22:24 or resid...B37 - 38
261(chain B and (resid 5:20 or resid 22:24 or resid...B40 - 50
271(chain B and (resid 5:20 or resid 22:24 or resid...B52 - 58
281(chain B and (resid 5:20 or resid 22:24 or resid...B60 - 73
291(chain B and (resid 5:20 or resid 22:24 or resid...B3 - 298
2101(chain B and (resid 5:20 or resid 22:24 or resid...B3 - 298
2111(chain B and (resid 5:20 or resid 22:24 or resid...B143 - 159
2121(chain B and (resid 5:20 or resid 22:24 or resid...B162 - 165
2131(chain B and (resid 5:20 or resid 22:24 or resid...B167 - 1838
2141(chain B and (resid 5:20 or resid 22:24 or resid...B220 - 28
2151(chain B and (resid 5:20 or resid 22:24 or resid...B220 - 230
2161(chain B and (resid 5:20 or resid 22:24 or resid...B233 - 23279
2171(chain B and (resid 5:20 or resid 22:24 or resid...B28276
2181(chain B and (resid 5:20 or resid 22:24 or resid...B278 - 279
2191(chain B and (resid 5:20 or resid 22:24 or resid...B282 - 291
2201(chain B and (resid 5:20 or resid 22:24 or resid...B293
2211(chain B and (resid 5:20 or resid 22:24 or resid...B295 - 298
311(chain C and (resid 5:20 or resid 22:24 or resid...C5 - 20
321(chain C and (resid 5:20 or resid 22:24 or resid...C22 - 24
331(chain C and (resid 5:20 or resid 22:24 or resid...C26 - 28
341(chain C and (resid 5:20 or resid 22:24 or resid...C30 - 31
351(chain C and (resid 5:20 or resid 22:24 or resid...C37 - 38
361(chain C and (resid 5:20 or resid 22:24 or resid...C40 - 50
371(chain C and (resid 5:20 or resid 22:24 or resid...C52 - 58
381(chain C and (resid 5:20 or resid 22:24 or resid...C60 - 73
391(chain C and (resid 5:20 or resid 22:24 or resid...C3 - 298
3101(chain C and (resid 5:20 or resid 22:24 or resid...C3 - 298
3111(chain C and (resid 5:20 or resid 22:24 or resid...C143 - 159
3121(chain C and (resid 5:20 or resid 22:24 or resid...C162 - 165
3131(chain C and (resid 5:20 or resid 22:24 or resid...C167 - 1838
3141(chain C and (resid 5:20 or resid 22:24 or resid...C220 - 28
3151(chain C and (resid 5:20 or resid 22:24 or resid...C220 - 230
3161(chain C and (resid 5:20 or resid 22:24 or resid...C233 - 23279
3171(chain C and (resid 5:20 or resid 22:24 or resid...C28276
3181(chain C and (resid 5:20 or resid 22:24 or resid...C278 - 279
3191(chain C and (resid 5:20 or resid 22:24 or resid...C282 - 291
3201(chain C and (resid 5:20 or resid 22:24 or resid...C293
3211(chain C and (resid 5:20 or resid 22:24 or resid...C295 - 298
411(chain D and (resid 5:20 or resid 22:24 or resid...D5 - 20
421(chain D and (resid 5:20 or resid 22:24 or resid...D22 - 24
431(chain D and (resid 5:20 or resid 22:24 or resid...D26 - 28
441(chain D and (resid 5:20 or resid 22:24 or resid...D30 - 31
451(chain D and (resid 5:20 or resid 22:24 or resid...D37 - 38
461(chain D and (resid 5:20 or resid 22:24 or resid...D40 - 50
471(chain D and (resid 5:20 or resid 22:24 or resid...D52 - 58
481(chain D and (resid 5:20 or resid 22:24 or resid...D60 - 73
491(chain D and (resid 5:20 or resid 22:24 or resid...D3 - 298
4101(chain D and (resid 5:20 or resid 22:24 or resid...D3 - 298
4111(chain D and (resid 5:20 or resid 22:24 or resid...D143 - 159
4121(chain D and (resid 5:20 or resid 22:24 or resid...D162 - 165
4131(chain D and (resid 5:20 or resid 22:24 or resid...D167 - 1838
4141(chain D and (resid 5:20 or resid 22:24 or resid...D220 - 28
4151(chain D and (resid 5:20 or resid 22:24 or resid...D220 - 230
4161(chain D and (resid 5:20 or resid 22:24 or resid...D233 - 23279
4171(chain D and (resid 5:20 or resid 22:24 or resid...D28276
4181(chain D and (resid 5:20 or resid 22:24 or resid...D278 - 279
4191(chain D and (resid 5:20 or resid 22:24 or resid...D282 - 291
4201(chain D and (resid 5:20 or resid 22:24 or resid...D293
4211(chain D and (resid 5:20 or resid 22:24 or resid...D295 - 298
511(chain E and (resid 5:20 or resid 22:24 or resid...E5 - 20
521(chain E and (resid 5:20 or resid 22:24 or resid...E22 - 24
531(chain E and (resid 5:20 or resid 22:24 or resid...E26 - 28
541(chain E and (resid 5:20 or resid 22:24 or resid...E30 - 31
551(chain E and (resid 5:20 or resid 22:24 or resid...E37 - 38
561(chain E and (resid 5:20 or resid 22:24 or resid...E40 - 50
571(chain E and (resid 5:20 or resid 22:24 or resid...E52 - 58
581(chain E and (resid 5:20 or resid 22:24 or resid...E60 - 73
591(chain E and (resid 5:20 or resid 22:24 or resid...E4 - 298
5101(chain E and (resid 5:20 or resid 22:24 or resid...E4 - 298
5111(chain E and (resid 5:20 or resid 22:24 or resid...E143 - 159
5121(chain E and (resid 5:20 or resid 22:24 or resid...E162 - 165
5131(chain E and (resid 5:20 or resid 22:24 or resid...E167 - 1838
5141(chain E and (resid 5:20 or resid 22:24 or resid...E220 - 28
5151(chain E and (resid 5:20 or resid 22:24 or resid...E220 - 230
5161(chain E and (resid 5:20 or resid 22:24 or resid...E233 - 23279
5171(chain E and (resid 5:20 or resid 22:24 or resid...E28276
5181(chain E and (resid 5:20 or resid 22:24 or resid...E278 - 279
5191(chain E and (resid 5:20 or resid 22:24 or resid...E282 - 291
5201(chain E and (resid 5:20 or resid 22:24 or resid...E293
5211(chain E and (resid 5:20 or resid 22:24 or resid...E295 - 298
611(chain F and (resid 5:20 or resid 22:24 or resid...F5 - 20
621(chain F and (resid 5:20 or resid 22:24 or resid...F22 - 24
631(chain F and (resid 5:20 or resid 22:24 or resid...F26 - 28
641(chain F and (resid 5:20 or resid 22:24 or resid...F30 - 31
651(chain F and (resid 5:20 or resid 22:24 or resid...F37 - 38
661(chain F and (resid 5:20 or resid 22:24 or resid...F40 - 50
671(chain F and (resid 5:20 or resid 22:24 or resid...F52 - 58
681(chain F and (resid 5:20 or resid 22:24 or resid...F60 - 73
691(chain F and (resid 5:20 or resid 22:24 or resid...F2 - 298
6101(chain F and (resid 5:20 or resid 22:24 or resid...F2 - 298
6111(chain F and (resid 5:20 or resid 22:24 or resid...F143 - 159
6121(chain F and (resid 5:20 or resid 22:24 or resid...F162 - 165
6131(chain F and (resid 5:20 or resid 22:24 or resid...F167 - 1838
6141(chain F and (resid 5:20 or resid 22:24 or resid...F220 - 28
6151(chain F and (resid 5:20 or resid 22:24 or resid...F220 - 230
6161(chain F and (resid 5:20 or resid 22:24 or resid...F233 - 23279
6171(chain F and (resid 5:20 or resid 22:24 or resid...F28276
6181(chain F and (resid 5:20 or resid 22:24 or resid...F278 - 279
6191(chain F and (resid 5:20 or resid 22:24 or resid...F282 - 291
6201(chain F and (resid 5:20 or resid 22:24 or resid...F293
6211(chain F and (resid 5:20 or resid 22:24 or resid...F295 - 298

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34161.215 Da / Num. of mol.: 6 / Mutation: H59N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 9 types, 1039 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 M Magnesium acetate, 8 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 60 mM L-Lysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2017
RadiationMonochromator: Double beam monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.67→46.142 Å / Num. obs: 229687 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.16
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.7076 / Num. unique obs: 22741 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIXdev_2398refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.67→46.142 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 11485 5 %
Rwork0.1625 218184 -
obs0.164 229669 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 24.8354 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.67→46.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13659 0 378 957 14994
Biso mean--44.38 32.15 -
Num. residues----1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214305
X-RAY DIFFRACTIONf_angle_d1.22419175
X-RAY DIFFRACTIONf_chiral_restr0.0762189
X-RAY DIFFRACTIONf_plane_restr0.0082441
X-RAY DIFFRACTIONf_dihedral_angle_d15.6228728
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7242X-RAY DIFFRACTION8.437TORSIONAL
12B7242X-RAY DIFFRACTION8.437TORSIONAL
13C7242X-RAY DIFFRACTION8.437TORSIONAL
14D7242X-RAY DIFFRACTION8.437TORSIONAL
15E7242X-RAY DIFFRACTION8.437TORSIONAL
16F7242X-RAY DIFFRACTION8.437TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.67-1.6890.28833800.25327209
1.689-1.70890.27133800.24047213
1.7089-1.72970.26983770.21487178
1.7297-1.75160.22513800.2117215
1.7516-1.77460.25213820.20167255
1.7746-1.79890.23163780.19387184
1.7989-1.82460.23343820.19857254
1.8246-1.85190.23343800.19367209
1.8519-1.88080.23023800.19087230
1.8808-1.91170.2373810.18237229
1.9117-1.94460.21823810.18037256
1.9446-1.980.22343800.17937215
1.98-2.01810.21013820.17117259
2.0181-2.05930.20873810.16637241
2.0593-2.1040.2143820.16357248
2.104-2.1530.18243800.15677215
2.153-2.20680.18873830.15657292
2.2068-2.26650.19333810.15547233
2.2665-2.33320.18293810.1527243
2.3332-2.40850.18963830.15247281
2.4085-2.49460.17533820.15217244
2.4946-2.59440.16893840.14527294
2.5944-2.71250.17183820.14667260
2.7125-2.85550.18483850.15077313
2.8555-3.03440.18453850.15397328
3.0344-3.26860.17833850.16067303
3.2686-3.59740.18283860.16357338
3.5974-4.11770.17753880.15437385
4.1177-5.18670.17473900.14817401
5.1867-7.470.18384040.16447659

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