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- PDB-7ko3: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88D mutant w... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7ko3
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88D 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: 2.22 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)207,41032
Polymers205,0276
Non-polymers2,38326
Water13,421745
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22211
Polymers68,3422
Non-polymers8809
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-32 kcal/mol
Surface area21650 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,06310
Polymers68,3422
Non-polymers7208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area21520 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,12511
Polymers68,3422
Non-polymers7829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-27 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.320, 232.260, 200.370
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 73 or (resid 74...
21(chain B and (resid 3 through 279 or (resid 280...
31(chain C and (resid 3 through 73 or (resid 74...
41(chain D and (resid 3 through 73 or (resid 74...
51(chain E and (resid 3 through 73 or (resid 74...
61(chain F and (resid 3 through 73 or (resid 74...

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
11LYSLYSTHRTHR(chain A and (resid 3 through 73 or (resid 74...AA3 - 7315 - 85
12LYSLYSLYSLYS(chain A and (resid 3 through 73 or (resid 74...AA7486
13LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 73 or (resid 74...AA3 - 29815 - 310
21LYSLYSSERSER(chain B and (resid 3 through 279 or (resid 280...BB3 - 27915 - 291
22LYSLYSLYSLYS(chain B and (resid 3 through 279 or (resid 280...BB280292
23LYSLYSPHEPHE(chain B and (resid 3 through 279 or (resid 280...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 279 or (resid 280...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 279 or (resid 280...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 279 or (resid 280...BB3 - 29815 - 310
31LYSLYSTHRTHR(chain C and (resid 3 through 73 or (resid 74...CC3 - 7315 - 85
32LYSLYSLYSLYS(chain C and (resid 3 through 73 or (resid 74...CC7486
33LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 73 or (resid 74...CC3 - 29815 - 310
41LYSLYSTHRTHR(chain D and (resid 3 through 73 or (resid 74...DD3 - 7315 - 85
42LYSLYSLYSLYS(chain D and (resid 3 through 73 or (resid 74...DD7486
43LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 73 or (resid 74...DD3 - 29815 - 310
51LYSLYSTHRTHR(chain E and (resid 3 through 73 or (resid 74...EE3 - 7315 - 85
52LYSLYSLYSLYS(chain E and (resid 3 through 73 or (resid 74...EE7486
53LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 73 or (resid 74...EE3 - 29815 - 310
61LYSLYSTHRTHR(chain F and (resid 3 through 73 or (resid 74...FF3 - 7315 - 85
62LYSLYSLYSLYS(chain F and (resid 3 through 73 or (resid 74...FF7486
63ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 310
65ASPASPPHEPHE(chain F and (resid 3 through 73 or (resid 74...FF2 - 29814 - 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 , 7 types, 771 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
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), 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 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: 2.22→43.82 Å / Num. obs: 1288408 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.998 / Net I/σ(I): 15.94
Reflection shellResolution: 2.22→2.299 Å / Rmerge(I) obs: 0.7434 / Num. unique obs: 9721 / % possible all: 99.98

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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: 2.22→43.82 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 4915 5 %
Rwork0.1568 93367 -
obs0.1592 98282 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.11 Å2 / Biso mean: 30.8805 Å2 / Biso min: 10.99 Å2
Refinement stepCycle: final / Resolution: 2.22→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13593 0 95 745 14433
Biso mean--44.23 35.64 -
Num. residues----1783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION4.379TORSIONAL
12B5358X-RAY DIFFRACTION4.379TORSIONAL
13C5358X-RAY DIFFRACTION4.379TORSIONAL
14D5358X-RAY DIFFRACTION4.379TORSIONAL
15E5358X-RAY DIFFRACTION4.379TORSIONAL
16F5358X-RAY DIFFRACTION4.379TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.22-2.250.25511640.1973111
2.25-2.270.2891590.1873036
2.27-2.30.27331630.18623089
2.3-2.330.25921620.18063072
2.33-2.360.25981620.17653093
2.36-2.390.23211620.17813076
2.39-2.430.23671650.17313121
2.43-2.460.26091590.18283032
2.46-2.50.23691640.17093110
2.5-2.540.23931630.16873096
2.54-2.590.19881630.14953103
2.59-2.630.19931610.13783049
2.63-2.680.19351630.14863103
2.68-2.740.22131640.15533110
2.74-2.80.21541610.15893068
2.8-2.860.23921650.16773124
2.86-2.930.19381620.16563087
2.93-3.010.22931630.17163095
3.01-3.10.25991630.17123107
3.1-3.20.2221640.17453098
3.2-3.320.20931640.16633122
3.32-3.450.22861640.17083123
3.45-3.610.20711640.16783102
3.61-3.80.17791640.15153124
3.8-4.030.17131660.13783148
4.03-4.340.15851640.13033120
4.34-4.780.15461660.13143162
4.78-5.470.18161660.14413158
5.47-6.890.20621690.1613210
6.89-100.18311760.13713318

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