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- PDB-7kls: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kls
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A 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 / 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: 2.59 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
DepositionOct 31, 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)206,98028
Polymers204,7096
Non-polymers2,27022
Water4,828268
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03310
Polymers68,2362
Non-polymers7968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area21570 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9148
Polymers68,2362
Non-polymers6786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-17 kcal/mol
Surface area21360 Å2
MethodPISA
3
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03310
Polymers68,2362
Non-polymers7968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-20 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.080, 231.290, 201.540
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 17 or (resid 18...
21(chain B and (resid 3 through 17 or (resid 18...
31(chain C and (resid 3 through 17 or (resid 18...
41(chain D and (resid 3 through 17 or (resid 18...
51(chain E and (resid 3 through 17 or (resid 18...
61(chain F and (resid 3 through 20 or (resid 21...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 17 or (resid 18...A3 - 17
121(chain A and (resid 3 through 17 or (resid 18...A18
131(chain A and (resid 3 through 17 or (resid 18...A4 - 298
141(chain A and (resid 3 through 17 or (resid 18...A4 - 298
151(chain A and (resid 3 through 17 or (resid 18...A4 - 298
161(chain A and (resid 3 through 17 or (resid 18...A4 - 298
211(chain B and (resid 3 through 17 or (resid 18...B3 - 17
221(chain B and (resid 3 through 17 or (resid 18...B18
231(chain B and (resid 3 through 17 or (resid 18...B3 - 298
241(chain B and (resid 3 through 17 or (resid 18...B3 - 298
251(chain B and (resid 3 through 17 or (resid 18...B3 - 298
311(chain C and (resid 3 through 17 or (resid 18...C3 - 17
321(chain C and (resid 3 through 17 or (resid 18...C18
331(chain C and (resid 3 through 17 or (resid 18...C4 - 298
341(chain C and (resid 3 through 17 or (resid 18...C4 - 298
351(chain C and (resid 3 through 17 or (resid 18...C4 - 298
411(chain D and (resid 3 through 17 or (resid 18...D3 - 17
421(chain D and (resid 3 through 17 or (resid 18...D18
431(chain D and (resid 3 through 17 or (resid 18...D3 - 298
441(chain D and (resid 3 through 17 or (resid 18...D3 - 298
451(chain D and (resid 3 through 17 or (resid 18...D3 - 298
461(chain D and (resid 3 through 17 or (resid 18...D3 - 298
511(chain E and (resid 3 through 17 or (resid 18...E3 - 17
521(chain E and (resid 3 through 17 or (resid 18...E18
531(chain E and (resid 3 through 17 or (resid 18...E3 - 298
541(chain E and (resid 3 through 17 or (resid 18...E3 - 298
551(chain E and (resid 3 through 17 or (resid 18...E3 - 298
561(chain E and (resid 3 through 17 or (resid 18...E3 - 298
611(chain F and (resid 3 through 20 or (resid 21...F3 - 20
621(chain F and (resid 3 through 20 or (resid 21...F21
631(chain F and (resid 3 through 20 or (resid 21...F3 - 298
641(chain F and (resid 3 through 20 or (resid 21...F3 - 298
651(chain F and (resid 3 through 20 or (resid 21...F3 - 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: 34118.191 Da / Num. of mol.: 6 / Mutation: H59A
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 , 5 types, 290 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 49.21 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.9 M Magnesium acetate, 8 % PEG8000, 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 7, 2017
RadiationMonochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→49.7 Å / Num. obs: 61928 / % possible obs: 99.52 % / Redundancy: 15 % / CC1/2: 0.992 / Net I/σ(I): 8.67
Reflection shellResolution: 2.59→2.683 Å / Rmerge(I) obs: 0.8254 / Num. unique obs: 6134 / % possible all: 99.68

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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: 2.59→49.7 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 3097 5 %
Rwork0.2108 58813 -
obs0.2129 61910 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.09 Å2 / Biso mean: 43.8972 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.59→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13555 0 101 268 13924
Biso mean--44.75 39.65 -
Num. residues----1779
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5286X-RAY DIFFRACTION5.287TORSIONAL
12B5286X-RAY DIFFRACTION5.287TORSIONAL
13C5286X-RAY DIFFRACTION5.287TORSIONAL
14D5286X-RAY DIFFRACTION5.287TORSIONAL
15E5286X-RAY DIFFRACTION5.287TORSIONAL
16F5286X-RAY DIFFRACTION5.287TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.59-2.630.29491390.2511264099
2.63-2.670.29871400.26442656100
2.67-2.720.311400.26162657100
2.72-2.770.32621390.26532641100
2.77-2.820.32091400.26882662100
2.82-2.880.33381400.26422655100
2.88-2.940.27521390.2472648100
2.94-3.010.31281400.24042657100
3.01-3.090.29191400.24112658100
3.09-3.170.28321400.23382655100
3.17-3.260.30481400.24752672100
3.26-3.370.29151400.24812664100
3.37-3.490.33391400.2282646100
3.49-3.630.271410.21982686100
3.63-3.790.28351400.20632650100
3.79-3.990.24221410.19842697100
3.99-4.240.21971420.1862268299
4.24-4.570.21841400.178266099
4.57-5.030.18651420.1747269799
5.03-5.760.23811420.1955270099
5.76-7.250.20571440.2012274099
7.25-9.350.17231480.1613279097

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