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- PDB-7lbd: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant w... -

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Basic information

Entry
Database: PDB / ID: 7lbd
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site in C2221 space group
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE
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: 1.99 Å
AuthorsSaran, S. / Yazdi, M.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: Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site
Authors: Yazdi, M.M. / Saran, S. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: 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)208,64353
Polymers205,0586
Non-polymers3,58547
Water13,944774
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,25137
Polymers136,7054
Non-polymers2,54633
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-20 kcal/mol
Surface area39590 Å2
MethodPISA
2
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,78432
Polymers136,7054
Non-polymers2,07928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area13510 Å2
ΔGint-21 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.120, 232.140, 201.810
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 24 or (resid 25...
21(chain B and (resid 3 through 24 or (resid 25...
31(chain C and (resid 3 through 24 or (resid 25...
41(chain D and (resid 3 through 24 or (resid 25...
51(chain E and (resid 3 through 24 or (resid 25...
61(chain F and (resid 3 through 31 or (resid 32...

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
11LYSLYSGLUGLU(chain A and (resid 3 through 24 or (resid 25...AA3 - 2415 - 36
12GLNGLNGLNGLN(chain A and (resid 3 through 24 or (resid 25...AA2537
13LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
17LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
21LYSLYSGLUGLU(chain B and (resid 3 through 24 or (resid 25...BB3 - 2415 - 36
22GLNGLNGLNGLN(chain B and (resid 3 through 24 or (resid 25...BB2537
23LYSLYSPHEPHE(chain B and (resid 3 through 24 or (resid 25...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 24 or (resid 25...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 24 or (resid 25...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 24 or (resid 25...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 24 or (resid 25...BB3 - 29815 - 310
31LYSLYSGLUGLU(chain C and (resid 3 through 24 or (resid 25...CC3 - 2415 - 36
32GLNGLNGLNGLN(chain C and (resid 3 through 24 or (resid 25...CC2537
33LYSLYSPHEPHE(chain C and (resid 3 through 24 or (resid 25...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 24 or (resid 25...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 24 or (resid 25...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 24 or (resid 25...CC3 - 29815 - 310
41LYSLYSGLUGLU(chain D and (resid 3 through 24 or (resid 25...DD3 - 2415 - 36
42GLNGLNGLNGLN(chain D and (resid 3 through 24 or (resid 25...DD2537
43LYSLYSPHEPHE(chain D and (resid 3 through 24 or (resid 25...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 24 or (resid 25...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 24 or (resid 25...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 24 or (resid 25...DD3 - 29815 - 310
47LYSLYSPHEPHE(chain D and (resid 3 through 24 or (resid 25...DD3 - 29815 - 310
51LYSLYSGLUGLU(chain E and (resid 3 through 24 or (resid 25...EE3 - 2415 - 36
52GLNGLNGLNGLN(chain E and (resid 3 through 24 or (resid 25...EE2537
53LYSLYSPHEPHE(chain E and (resid 3 through 24 or (resid 25...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 24 or (resid 25...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 24 or (resid 25...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 24 or (resid 25...EE3 - 29815 - 310
57LYSLYSPHEPHE(chain E and (resid 3 through 24 or (resid 25...EE3 - 29815 - 310
61LYSLYSILEILE(chain F and (resid 3 through 31 or (resid 32...FF3 - 3115 - 43
62LYSLYSLYSLYS(chain F and (resid 3 through 31 or (resid 32...FF3244
63LYSLYSPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 31 or (resid 32...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: 34176.293 Da / Num. of mol.: 6 / Mutation: H59K
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, 821 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 49.4 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 12 % PEG8000, 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: Jan 20, 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: 1.99→43.94 Å / Num. obs: 136388 / % possible obs: 91.19 % / Redundancy: 15 % / CC1/2: 0.991 / CC star: 0.998 / Rrim(I) all: 0.2399 / Net I/σ(I): 6.12
Reflection shellResolution: 1.99→2.061 Å / Rmerge(I) obs: 1.619 / Num. unique obs: 38731 / CC1/2: 0.389 / CC star: 0.748 / Rpim(I) all: 0.7488 / % possible all: 97.17

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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: 1.99→43.94 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 6820 5 %
Rwork0.1914 129544 -
obs0.1929 136364 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.33 Å2 / Biso mean: 34.2619 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.99→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13575 0 232 774 14581
Biso mean--53.11 39.25 -
Num. residues----1776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5352X-RAY DIFFRACTION2.545TORSIONAL
12B5352X-RAY DIFFRACTION2.545TORSIONAL
13C5352X-RAY DIFFRACTION2.545TORSIONAL
14D5352X-RAY DIFFRACTION2.545TORSIONAL
15E5352X-RAY DIFFRACTION2.545TORSIONAL
16F5352X-RAY DIFFRACTION2.545TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.010.37442250.359442694494100
2.01-2.040.37612250.339142824507100
2.04-2.060.37062270.324643134540100
2.06-2.090.3312250.305742744499100
2.09-2.110.32532240.28142544478100
2.11-2.140.29792260.266242964522100
2.14-2.170.312270.251742984525100
2.17-2.210.27392260.243942914517100
2.21-2.240.26542260.237743084534100
2.24-2.280.26892240.229342464470100
2.28-2.320.26862260.224942914517100
2.32-2.360.28292270.217443144541100
2.36-2.40.26272250.226942804505100
2.4-2.450.27862270.208443164543100
2.45-2.510.25812270.203343024529100
2.51-2.570.23282250.196142874512100
2.57-2.630.20622280.190143194547100
2.63-2.70.24192260.187342954521100
2.7-2.780.22282260.187443084534100
2.78-2.870.22092280.184943214549100
2.87-2.970.2292260.187442994525100
2.97-3.090.25322290.19343464575100
3.09-3.230.23032270.190743134540100
3.23-3.40.21392290.186643554584100
3.4-3.620.22412280.183343284556100
3.62-3.890.18852290.164343544583100
3.89-4.290.16752290.15044342457199
4.29-4.910.1552290.14614360458999
4.91-6.180.17682330.169544244657100
6.18-43.940.17092410.16174559480099
Refinement TLS params.Method: refined / Origin x: 2.0875 Å / Origin y: 105.9683 Å / Origin z: -29.8072 Å
111213212223313233
T0.2568 Å20.0334 Å20.0144 Å2-0.2538 Å20.0245 Å2--0.2628 Å2
L0.164 °20.1974 °2-0.0818 °2-0.2762 °2-0.154 °2--0.146 °2
S-0.0204 Å °0.0092 Å °0.006 Å °-0.0268 Å °0.0291 Å °0.0184 Å °-0.0021 Å °-0.0317 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 298
2X-RAY DIFFRACTION1allB3 - 298
3X-RAY DIFFRACTION1allC3 - 298
4X-RAY DIFFRACTION1allD3 - 298
5X-RAY DIFFRACTION1allE3 - 298
6X-RAY DIFFRACTION1allF3 - 298
7X-RAY DIFFRACTION1allS4 - 861
8X-RAY DIFFRACTION1allG1 - 6
9X-RAY DIFFRACTION1allH1 - 16
10X-RAY DIFFRACTION1allI1 - 6
11X-RAY DIFFRACTION1allJ1 - 10
12X-RAY DIFFRACTION1allK1 - 10

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