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- PDB-7kkt: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kkt
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and R,R-bislysine 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
Chem-3VN / 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: 1.71 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: A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS
Authors: Saran, S. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionOct 28, 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)209,29361
Polymers205,1176
Non-polymers4,17655
Water26,6621480
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,36114
Polymers68,3722
Non-polymers98912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-39 kcal/mol
Surface area21900 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86624
Polymers68,3722
Non-polymers1,49322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-68 kcal/mol
Surface area22020 Å2
MethodPISA
3
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06623
Polymers68,3722
Non-polymers1,69421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-19 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.020, 225.470, 200.420
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 or resid 5:20 or resid...
21(chain B and (resid 3 or resid 5:20 or resid...
31(chain C and (resid 3 or resid 5:20 or resid...
41(chain D and (resid 3 or resid 5:20 or resid...
51(chain E and (resid 3 or resid 5:20 or resid...
61(chain F and (resid 3 or resid 5:20 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 or resid 5:20 or resid...A3
121(chain A and (resid 3 or resid 5:20 or resid...A5 - 20
131(chain A and (resid 3 or resid 5:20 or resid...A22 - 24
141(chain A and (resid 3 or resid 5:20 or resid...A26 - 31
151(chain A and (resid 3 or resid 5:20 or resid...A0
161(chain A and (resid 3 or resid 5:20 or resid...A52 - 56
171(chain A and (resid 3 or resid 5:20 or resid...A3 - 298
181(chain A and (resid 3 or resid 5:20 or resid...A75 - 97
191(chain A and (resid 3 or resid 5:20 or resid...A3 - 298
1101(chain A and (resid 3 or resid 5:20 or resid...A3 - 298
1111(chain A and (resid 3 or resid 5:20 or resid...A162 - 165
1121(chain A and (resid 3 or resid 5:20 or resid...A233 - 231
1131(chain A and (resid 3 or resid 5:20 or resid...A233 - 234
1141(chain A and (resid 3 or resid 5:20 or resid...A236 - 238
1151(chain A and (resid 3 or resid 5:20 or resid...A240 - 266
1161(chain A and (resid 3 or resid 5:20 or resid...A282 - 289
1171(chain A and (resid 3 or resid 5:20 or resid...A289 - 296
1181(chain A and (resid 3 or resid 5:20 or resid...A289 - 291
1191(chain A and (resid 3 or resid 5:20 or resid...A293
1201(chain A and (resid 3 or resid 5:20 or resid...A295 - 298
211(chain B and (resid 3 or resid 5:20 or resid...B3
221(chain B and (resid 3 or resid 5:20 or resid...B5 - 20
231(chain B and (resid 3 or resid 5:20 or resid...B22 - 24
241(chain B and (resid 3 or resid 5:20 or resid...B26 - 31
251(chain B and (resid 3 or resid 5:20 or resid...B0
261(chain B and (resid 3 or resid 5:20 or resid...B52 - 56
271(chain B and (resid 3 or resid 5:20 or resid...B-7 - 298
281(chain B and (resid 3 or resid 5:20 or resid...B75 - 97
291(chain B and (resid 3 or resid 5:20 or resid...B-7 - 298
2101(chain B and (resid 3 or resid 5:20 or resid...B-7 - 298
2111(chain B and (resid 3 or resid 5:20 or resid...B162 - 165
2121(chain B and (resid 3 or resid 5:20 or resid...B233 - 231
2131(chain B and (resid 3 or resid 5:20 or resid...B233 - 234
2141(chain B and (resid 3 or resid 5:20 or resid...B236 - 238
2151(chain B and (resid 3 or resid 5:20 or resid...B240 - 266
2161(chain B and (resid 3 or resid 5:20 or resid...B282 - 289
2171(chain B and (resid 3 or resid 5:20 or resid...B289 - 296
2181(chain B and (resid 3 or resid 5:20 or resid...B289 - 291
2191(chain B and (resid 3 or resid 5:20 or resid...B293
2201(chain B and (resid 3 or resid 5:20 or resid...B295 - 298
311(chain C and (resid 3 or resid 5:20 or resid...C3
321(chain C and (resid 3 or resid 5:20 or resid...C5 - 20
331(chain C and (resid 3 or resid 5:20 or resid...C22 - 24
341(chain C and (resid 3 or resid 5:20 or resid...C26 - 31
351(chain C and (resid 3 or resid 5:20 or resid...C0
361(chain C and (resid 3 or resid 5:20 or resid...C52 - 56
371(chain C and (resid 3 or resid 5:20 or resid...C-7 - 298
381(chain C and (resid 3 or resid 5:20 or resid...C75 - 97
391(chain C and (resid 3 or resid 5:20 or resid...C-7 - 298
3101(chain C and (resid 3 or resid 5:20 or resid...C-7 - 298
3111(chain C and (resid 3 or resid 5:20 or resid...C162 - 165
3121(chain C and (resid 3 or resid 5:20 or resid...C233 - 231
3131(chain C and (resid 3 or resid 5:20 or resid...C233 - 234
3141(chain C and (resid 3 or resid 5:20 or resid...C236 - 238
3151(chain C and (resid 3 or resid 5:20 or resid...C240 - 266
3161(chain C and (resid 3 or resid 5:20 or resid...C282 - 289
3171(chain C and (resid 3 or resid 5:20 or resid...C289 - 296
3181(chain C and (resid 3 or resid 5:20 or resid...C289 - 291
3191(chain C and (resid 3 or resid 5:20 or resid...C293
3201(chain C and (resid 3 or resid 5:20 or resid...C295 - 298
411(chain D and (resid 3 or resid 5:20 or resid...D3
421(chain D and (resid 3 or resid 5:20 or resid...D5 - 20
431(chain D and (resid 3 or resid 5:20 or resid...D22 - 24
441(chain D and (resid 3 or resid 5:20 or resid...D26 - 31
451(chain D and (resid 3 or resid 5:20 or resid...D0
461(chain D and (resid 3 or resid 5:20 or resid...D52 - 56
471(chain D and (resid 3 or resid 5:20 or resid...D3 - 298
481(chain D and (resid 3 or resid 5:20 or resid...D75 - 97
491(chain D and (resid 3 or resid 5:20 or resid...D3 - 298
4101(chain D and (resid 3 or resid 5:20 or resid...D3 - 298
4111(chain D and (resid 3 or resid 5:20 or resid...D162 - 165
4121(chain D and (resid 3 or resid 5:20 or resid...D233 - 231
4131(chain D and (resid 3 or resid 5:20 or resid...D233 - 234
4141(chain D and (resid 3 or resid 5:20 or resid...D236 - 238
4151(chain D and (resid 3 or resid 5:20 or resid...D240 - 266
4161(chain D and (resid 3 or resid 5:20 or resid...D282 - 289
4171(chain D and (resid 3 or resid 5:20 or resid...D289 - 296
4181(chain D and (resid 3 or resid 5:20 or resid...D289 - 291
4191(chain D and (resid 3 or resid 5:20 or resid...D293
4201(chain D and (resid 3 or resid 5:20 or resid...D295 - 298
511(chain E and (resid 3 or resid 5:20 or resid...E3
521(chain E and (resid 3 or resid 5:20 or resid...E5 - 20
531(chain E and (resid 3 or resid 5:20 or resid...E22 - 24
541(chain E and (resid 3 or resid 5:20 or resid...E26 - 31
551(chain E and (resid 3 or resid 5:20 or resid...E0
561(chain E and (resid 3 or resid 5:20 or resid...E52 - 56
571(chain E and (resid 3 or resid 5:20 or resid...E2 - 298
581(chain E and (resid 3 or resid 5:20 or resid...E75 - 97
591(chain E and (resid 3 or resid 5:20 or resid...E2 - 298
5101(chain E and (resid 3 or resid 5:20 or resid...E2 - 298
5111(chain E and (resid 3 or resid 5:20 or resid...E162 - 165
5121(chain E and (resid 3 or resid 5:20 or resid...E233 - 231
5131(chain E and (resid 3 or resid 5:20 or resid...E233 - 234
5141(chain E and (resid 3 or resid 5:20 or resid...E236 - 238
5151(chain E and (resid 3 or resid 5:20 or resid...E240 - 266
5161(chain E and (resid 3 or resid 5:20 or resid...E282 - 289
5171(chain E and (resid 3 or resid 5:20 or resid...E289 - 296
5181(chain E and (resid 3 or resid 5:20 or resid...E289 - 291
5191(chain E and (resid 3 or resid 5:20 or resid...E293
5201(chain E and (resid 3 or resid 5:20 or resid...E295 - 298
611(chain F and (resid 3 or resid 5:20 or resid...F3
621(chain F and (resid 3 or resid 5:20 or resid...F5 - 20
631(chain F and (resid 3 or resid 5:20 or resid...F22 - 24
641(chain F and (resid 3 or resid 5:20 or resid...F26 - 31
651(chain F and (resid 3 or resid 5:20 or resid...F0
661(chain F and (resid 3 or resid 5:20 or resid...F52 - 56
671(chain F and (resid 3 or resid 5:20 or resid...F3 - 298
681(chain F and (resid 3 or resid 5:20 or resid...F75 - 97
691(chain F and (resid 3 or resid 5:20 or resid...F3 - 298
6101(chain F and (resid 3 or resid 5:20 or resid...F3 - 298
6111(chain F and (resid 3 or resid 5:20 or resid...F162 - 165
6121(chain F and (resid 3 or resid 5:20 or resid...F233 - 231
6131(chain F and (resid 3 or resid 5:20 or resid...F233 - 234
6141(chain F and (resid 3 or resid 5:20 or resid...F236 - 238
6151(chain F and (resid 3 or resid 5:20 or resid...F240 - 266
6161(chain F and (resid 3 or resid 5:20 or resid...F282 - 289
6171(chain F and (resid 3 or resid 5:20 or resid...F289 - 296
6181(chain F and (resid 3 or resid 5:20 or resid...F289 - 291
6191(chain F and (resid 3 or resid 5:20 or resid...F293
6201(chain F and (resid 3 or resid 5:20 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: 34186.246 Da / Num. of mol.: 6 / Mutation: N84D
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, 1535 molecules

#2: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30N4O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1480 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.7 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4), 120 mMR,R-BisLysine

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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: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 5, 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: 1.71→49.129 Å / Num. obs: 203207 / % possible obs: 98.3 % / Redundancy: 15 % / Biso Wilson estimate: 19.48 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.43
Reflection shellResolution: 1.71→1.771 Å / Rmerge(I) obs: 0.3301 / Num. unique obs: 17773 / % possible all: 86.34

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2398refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.71→49.129 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 10156 5 %
Rwork0.1636 192999 -
obs0.1652 203155 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.76 Å2 / Biso mean: 21.9434 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.71→49.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13852 0 267 1480 15599
Biso mean--34.53 30.98 -
Num. residues----1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914340
X-RAY DIFFRACTIONf_angle_d1.03619305
X-RAY DIFFRACTIONf_chiral_restr0.0662204
X-RAY DIFFRACTIONf_plane_restr0.0072461
X-RAY DIFFRACTIONf_dihedral_angle_d15.558710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7381X-RAY DIFFRACTION4.586TORSIONAL
12B7381X-RAY DIFFRACTION4.586TORSIONAL
13C7381X-RAY DIFFRACTION4.586TORSIONAL
14D7381X-RAY DIFFRACTION4.586TORSIONAL
15E7381X-RAY DIFFRACTION4.586TORSIONAL
16F7381X-RAY DIFFRACTION4.586TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.71-1.72950.3913000.3894572788
1.7295-1.74980.37392840.3807538283
1.7498-1.77110.39143030.3124575888
1.7711-1.79360.24213380.19216429100
1.7936-1.81720.22613410.1716469100
1.8172-1.84210.2223430.1796517100
1.8421-1.86840.22093410.18166483100
1.8684-1.89630.2843410.23176484100
1.8963-1.92590.43293310.3479629197
1.9259-1.95750.23863410.206647599
1.9575-1.99120.21263390.16376479100
1.9912-2.02740.20573440.15426535100
2.0274-2.06640.22013400.1991645299
2.0664-2.10860.23583400.18226476100
2.1086-2.15450.18513440.14416529100
2.1545-2.20460.19943420.14846495100
2.2046-2.25970.26143350.2182636598
2.2597-2.32080.19653440.15196527100
2.3208-2.38910.19533420.14766516100
2.3891-2.46620.17913440.14846521100
2.4662-2.55430.15913440.13926545100
2.5543-2.65660.18093470.14296586100
2.6566-2.77750.18023400.1476465100
2.7775-2.92390.19263470.15386588100
2.9239-3.10710.19493450.1546568100
3.1071-3.34690.18853480.15796604100
3.3469-3.68370.16553450.1527655999
3.6837-4.21640.15133470.13426595100
4.2164-5.31130.15133530.12956709100
5.3113-7.650.15143630.14576870100

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