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- PDB-7ko1: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88D mutant w... -

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Basic information

Entry
Database: PDB / ID: 7ko1
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88D mutant with pyruvate bound in the active site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / 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 / 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: 2.5 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.
Authors: Saran, S. / Majdi Yazdi, M. / Chung, I. / Sanders, D.A.R.
History
DepositionNov 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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)206,58229
Polymers205,0276
Non-polymers1,55423
Water10,106561
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7758
Polymers68,3422
Non-polymers4326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-26 kcal/mol
Surface area21780 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,89610
Polymers68,3422
Non-polymers5538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-31 kcal/mol
Surface area21600 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,91111
Polymers68,3422
Non-polymers5689
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-35 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 232.650, 201.860
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 3 through 230 or (resid 231...
21(chain B and (resid 3 through 293 or (resid 294...
31(chain C and (resid 3 through 230 or (resid 231...
41(chain D and (resid 3 through 165 or (resid 166...
51(chain E and (resid 3 through 230 or (resid 231...
61(chain F and (resid 3 through 165 or (resid 166...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYR(chain A and (resid 3 through 230 or (resid 231...AA3 - 23015 - 242
12LYSLYSLYSLYS(chain A and (resid 3 through 230 or (resid 231...AA231243
13LYSLYSPHEPHE(chain A and (resid 3 through 230 or (resid 231...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 230 or (resid 231...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 230 or (resid 231...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 230 or (resid 231...AA3 - 29815 - 310
21LYSLYSTYRTYR(chain B and (resid 3 through 293 or (resid 294...BB3 - 29315 - 305
22LYSLYSLYSLYS(chain B and (resid 3 through 293 or (resid 294...BB294306
23LYSLYSPHEPHE(chain B and (resid 3 through 293 or (resid 294...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 293 or (resid 294...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 293 or (resid 294...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 293 or (resid 294...BB3 - 29815 - 310
31LYSLYSTYRTYR(chain C and (resid 3 through 230 or (resid 231...CC3 - 23015 - 242
32LYSLYSLYSLYS(chain C and (resid 3 through 230 or (resid 231...CC231243
33LYSLYSPHEPHE(chain C and (resid 3 through 230 or (resid 231...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 230 or (resid 231...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 230 or (resid 231...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 230 or (resid 231...CC3 - 29815 - 310
41LYSLYSVALVAL(chain D and (resid 3 through 165 or (resid 166...DD3 - 16515 - 177
42KPIKPIKPIKPI(chain D and (resid 3 through 165 or (resid 166...DD166178
43ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
44ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
45ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
46ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
47ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
48ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
49ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
410ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
411ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
412ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
413ASPASPPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD2 - 29814 - 310
51LYSLYSTYRTYR(chain E and (resid 3 through 230 or (resid 231...EE3 - 23015 - 242
52LYSLYSLYSLYS(chain E and (resid 3 through 230 or (resid 231...EE231243
53LYSLYSPHEPHE(chain E and (resid 3 through 230 or (resid 231...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 230 or (resid 231...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 230 or (resid 231...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 230 or (resid 231...EE3 - 29815 - 310
61LYSLYSVALVAL(chain F and (resid 3 through 165 or (resid 166...FF3 - 16515 - 177
62KPIKPIKPIKPI(chain F and (resid 3 through 165 or (resid 166...FF166178
63LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
67LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
68LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
69LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
610LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
611LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
612LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
613LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
614LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310
615LYSLYSPHEPHE(chain F and (resid 3 through 165 or (resid 166...FF3 - 29815 - 310

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34171.234 Da / Num. of mol.: 6 / Mutation: E88D
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 , 6 types, 584 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 10 % PEG 8000, 0.1 M Sodium acetate (pH 7.4)

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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 S 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationMonochromator: double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→44 Å / Num. obs: 68720 / % possible obs: 98.7 % / Redundancy: 15 % / CC1/2: 0.998 / Net I/σ(I): 18.31
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.675 / Num. unique obs: 6214 / % possible all: 89.98

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.5→44 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 3434 5 %
Rwork0.1789 65273 -
obs0.181 68707 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.74 Å2 / Biso mean: 37.2507 Å2 / Biso min: 19.24 Å2
Refinement stepCycle: final / Resolution: 2.5→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13618 0 98 561 14277
Biso mean--46.85 37.29 -
Num. residues----1777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION2.096TORSIONAL
12B5358X-RAY DIFFRACTION2.096TORSIONAL
13C5358X-RAY DIFFRACTION2.096TORSIONAL
14D5358X-RAY DIFFRACTION2.096TORSIONAL
15E5358X-RAY DIFFRACTION2.096TORSIONAL
16F5358X-RAY DIFFRACTION2.096TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.530.30681150.2348219083
2.53-2.570.27031270.2144242093
2.57-2.610.27511360.2043257698
2.61-2.650.27511360.2057258699
2.65-2.690.23461370.1998260899
2.69-2.740.27421370.2008260599
2.74-2.790.2971360.205257399
2.79-2.840.27611380.1988262199
2.84-2.90.28171360.20752595100
2.9-2.960.25861380.2016262699
2.96-3.030.26981390.21892642100
3.03-3.110.2871360.2109258099
3.11-3.190.28051390.20542628100
3.19-3.290.26621380.2063263399
3.29-3.390.24421380.20082621100
3.39-3.510.25971390.19382631100
3.51-3.650.22561390.18412639100
3.65-3.820.19941390.17572646100
3.82-4.020.19841390.16112648100
4.02-4.270.17661400.15262658100
4.27-4.60.16571390.14492639100
4.6-5.070.17941410.14732681100
5.07-5.80.19531410.16622684100
5.8-7.30.20591440.16622721100
7.3-100.1461470.14382822100

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