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- PDB-7knz: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7knz
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and R,R-bislysine at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


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: 2.28 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: 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)209,77968
Polymers204,7636
Non-polymers5,01562
Water15,331851
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,05826
Polymers68,2542
Non-polymers1,80324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-10 kcal/mol
Surface area21330 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,94823
Polymers68,2542
Non-polymers1,69421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-17 kcal/mol
Surface area22240 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,77319
Polymers68,2542
Non-polymers1,51817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-17 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.120, 231.210, 200.120
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 112 or (resid 113...
21(chain B and (resid 3 through 17 or (resid 18...
31(chain C and (resid 3 through 20 or (resid 21...
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:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASN(chain A and (resid 3 through 112 or (resid 113...AA3 - 11215 - 124
12LYSLYS(chain A and (resid 3 through 112 or (resid 113...AA113125
13PHEPHE(chain A and (resid 3 through 112 or (resid 113...AA3 - 29815 - 310
14PHEPHE(chain A and (resid 3 through 112 or (resid 113...AA3 - 29815 - 310
15PHEPHE(chain A and (resid 3 through 112 or (resid 113...AA3 - 29815 - 310
16PHEPHE(chain A and (resid 3 through 112 or (resid 113...AA3 - 29815 - 310
17PHEPHE(chain A and (resid 3 through 112 or (resid 113...AA3 - 29815 - 310
21PHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 1715 - 29
22LYSLYS(chain B and (resid 3 through 17 or (resid 18...BB1830
23PHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
24PHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
25PHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
31GLYGLY(chain C and (resid 3 through 20 or (resid 21...CC3 - 2015 - 32
32LYSLYS(chain C and (resid 3 through 20 or (resid 21...CC2133
33PHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
34PHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
35PHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
36PHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
37PHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
41PHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 1715 - 29
42LYSLYS(chain D and (resid 3 through 17 or (resid 18...DD1830
43PHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
44PHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
45PHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
46PHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
51PHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 1715 - 29
52LYSLYS(chain E and (resid 3 through 17 or (resid 18...EE1830
53PHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
54PHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
55PHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
56PHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
61GLYGLY(chain F and (resid 3 through 20 or (resid 21...FF3 - 2015 - 32
62LYSLYS(chain F and (resid 3 through 20 or (resid 21...FF2133
63PHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
64PHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
65PHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
66PHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
67PHEPHE(chain F and (resid 3 through 20 or (resid 21...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: 34127.223 Da / Num. of mol.: 6 / Mutation: E88A
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 , 8 types, 913 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
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), 120 mM R,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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 29, 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: 2.28→45.91 Å / Num. obs: 89981 / % possible obs: 99.9 % / Redundancy: 15 % / CC1/2: 0.995 / Net I/σ(I): 10.56
Reflection shellResolution: 2.28→2.361 Å / Rmerge(I) obs: 0.8348 / Num. unique obs: 8836 / % possible all: 99.18

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Processing

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

4ly8


Resolution: 2.28→45.91 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 4498 5 %
Rwork0.1795 85465 -
obs0.1813 89963 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.02 Å2 / Biso mean: 31.4849 Å2 / Biso min: 16.42 Å2
Refinement stepCycle: final / Resolution: 2.28→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13566 0 327 851 14744
Biso mean--40.19 35.63 -
Num. residues----1776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION3.47TORSIONAL
12B5358X-RAY DIFFRACTION3.47TORSIONAL
13C5358X-RAY DIFFRACTION3.47TORSIONAL
14D5358X-RAY DIFFRACTION3.47TORSIONAL
15E5358X-RAY DIFFRACTION3.47TORSIONAL
16F5358X-RAY DIFFRACTION3.47TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.310.31631440.2846274298
2.31-2.330.32931490.26732825100
2.33-2.360.29791480.24122826100
2.36-2.390.25051480.22432799100
2.39-2.420.2541500.22042861100
2.42-2.460.28651470.21142787100
2.46-2.490.25231490.19772828100
2.49-2.530.22551490.19862830100
2.53-2.570.23121500.18732842100
2.57-2.610.23951480.18132826100
2.61-2.650.24471500.18252836100
2.65-2.70.21731470.17972809100
2.7-2.760.2231510.19122862100
2.76-2.810.24741480.18382804100
2.81-2.870.23361490.19322842100
2.87-2.940.25231510.18532864100
2.94-3.010.20771480.18152818100
3.01-3.090.21831490.17552833100
3.09-3.190.23581500.17872850100
3.19-3.290.19121480.18092832100
3.29-3.410.23791520.18762885100
3.41-3.540.24191490.18192836100
3.54-3.70.1721510.17072861100
3.7-3.90.19261500.16222845100
3.9-4.140.18911510.15432864100
4.14-4.460.17791520.1542887100
4.46-4.910.17711520.15282896100
4.91-5.620.19641530.1732900100
5.62-7.080.21761540.18282929100
7.08-100.18831610.1593046100

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