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- PDB-7ku6: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56N mutant w... -

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Basic information

Entry
Database: PDB / ID: 7ku6
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56N mutant with pyruvate bound in the active site
Components(4-hydroxy-tetrahydrodipicolinate ...) x 2
KeywordsLYASE
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
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: 2.81 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: ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS
Authors: Saran, S. / Skovpen, Y. / Yazdi, M.M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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)205,97619
Polymers204,8296
Non-polymers1,14713
Water543
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)137,46714
Polymers136,6454
Non-polymers82210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)137,01810
Polymers136,3694
Non-polymers6496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)85.750, 234.420, 202.890
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 31 or (resid 32...
21(chain B and (resid 3 through 31 or (resid 32...
31(chain C and (resid 3 through 165 or resid 167 through 298))
41(chain D and (resid 3 through 31 or (resid 32...
51(chain E and (resid 3 through 31 or (resid 32...
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
11LYSLYSILEILE(chain A and (resid 3 through 31 or (resid 32...AA3 - 3115 - 43
12LYSLYSLYSLYS(chain A and (resid 3 through 31 or (resid 32...AA3244
13LYSLYSPHEPHE(chain A and (resid 3 through 31 or (resid 32...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 31 or (resid 32...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 31 or (resid 32...AA3 - 29815 - 310
21LYSLYSILEILE(chain B and (resid 3 through 31 or (resid 32...BB3 - 3115 - 43
22LYSLYSLYSLYS(chain B and (resid 3 through 31 or (resid 32...BB3244
23LYSLYSPHEPHE(chain B and (resid 3 through 31 or (resid 32...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 31 or (resid 32...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 31 or (resid 32...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 31 or (resid 32...BB3 - 29815 - 310
31LYSLYSVALVAL(chain C and (resid 3 through 165 or resid 167 through 298))CC3 - 16515 - 177
32GLUGLUPHEPHE(chain C and (resid 3 through 165 or resid 167 through 298))CC167 - 298179 - 310
41LYSLYSILEILE(chain D and (resid 3 through 31 or (resid 32...DD3 - 3115 - 43
42LYSLYSLYSLYS(chain D and (resid 3 through 31 or (resid 32...DD3244
43LYSLYSPHEPHE(chain D and (resid 3 through 31 or (resid 32...DD3 - 29815 - 310
51LYSLYSILEILE(chain E and (resid 3 through 31 or (resid 32...EE3 - 3115 - 43
52LYSLYSLYSLYS(chain E and (resid 3 through 31 or (resid 32...EE3244
53LYSLYSPHEPHE(chain E and (resid 3 through 31 or (resid 32...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 31 or (resid 32...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 31 or (resid 32...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
63ASPASPPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF2 - 29814 - 310
65ASPASPPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF2 - 29814 - 310
66ASPASPPHEPHE(chain F and (resid 3 through 31 or (resid 32...FF2 - 29814 - 310

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Components

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4-hydroxy-tetrahydrodipicolinate ... , 2 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34161.215 Da / Num. of mol.: 4 / Mutation: H56N
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
#2: Protein 4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34092.180 Da / Num. of mol.: 2 / Mutation: H56N
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 , 4 types, 16 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 12 % PEG 8000, 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: 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: 2.81→46.55 Å / Num. obs: 107327 / % possible obs: 99.66 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 10.2
Reflection shellResolution: 2.81→2.91 Å / Rmerge(I) obs: 0.426 / Num. unique obs: 4956 / % possible all: 99.58

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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: 2.81→46.55 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 2501 5 %
Rwork0.2179 47523 -
obs0.22 50024 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.74 Å2 / Biso mean: 35.6552 Å2 / Biso min: 21.1 Å2
Refinement stepCycle: final / Resolution: 2.81→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13627 0 73 3 13703
Biso mean--49.08 22.73 -
Num. residues----1777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5316X-RAY DIFFRACTION2.82TORSIONAL
12B5316X-RAY DIFFRACTION2.82TORSIONAL
13C5316X-RAY DIFFRACTION2.82TORSIONAL
14D5316X-RAY DIFFRACTION2.82TORSIONAL
15E5316X-RAY DIFFRACTION2.82TORSIONAL
16F5316X-RAY DIFFRACTION2.82TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.81-2.860.3251380.27342629100
2.86-2.920.31781360.27652582100
2.92-2.990.31461380.26912626100
2.99-3.060.32891390.2862262999
3.06-3.130.34621360.27652588100
3.13-3.220.29281390.26092639100
3.22-3.310.3491380.25852616100
3.31-3.420.30981370.25812622100
3.42-3.540.29391380.2522617100
3.54-3.680.31661390.23192636100
3.68-3.850.27241380.21642628100
3.85-4.050.23561400.1942646100
4.05-4.310.2261380.1817262699
4.31-4.640.20521380.1783263099
4.64-5.10.20211400.17912665100
5.1-5.840.23471400.18542668100
5.84-7.350.19661430.18852708100
7.36-100.19621460.1807276898
Refinement TLS params.Method: refined / Origin x: 2.1601 Å / Origin y: 10.528 Å / Origin z: 29.9714 Å
111213212223313233
T0.2773 Å2-0.0581 Å2-0.0261 Å2-0.2545 Å20.0402 Å2--0.2731 Å2
L0.2723 °2-0.2946 °20.0468 °2-0.307 °2-0.1339 °2--0.1576 °2
S-0.0343 Å °0.015 Å °-0.0204 Å °0.0407 Å °0.0332 Å °0.0136 Å °0.0148 Å °-0.0416 Å °0.0091 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 DIFFRACTION1allF2 - 298
7X-RAY DIFFRACTION1allG1 - 6
8X-RAY DIFFRACTION1allH1 - 5
9X-RAY DIFFRACTION1allJ1 - 2
10X-RAY DIFFRACTION1allS1 - 3

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