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- PDB-7klt: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant w... -

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Basic information

Entry
Database: PDB / ID: 7klt
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
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: 1.97 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
DepositionNov 1, 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)210,04772
Polymers204,9676
Non-polymers5,08066
Water12,268681
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,36828
Polymers68,3222
Non-polymers2,04626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-22 kcal/mol
Surface area23170 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,98823
Polymers68,3222
Non-polymers1,66621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-11 kcal/mol
Surface area22520 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,69121
Polymers68,3222
Non-polymers1,36919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-19 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.350, 233.390, 202.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34161.215 Da / Num. of mol.: 6 / Mutation: H59N
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, 747 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 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 PILATUS 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: 1.97→44.14 Å / Num. obs: 142117 / % possible obs: 99.8 % / Redundancy: 15 % / CC1/2: 0.998 / Net I/σ(I): 12.06
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.9167 / Num. unique obs: 14129 / % possible all: 99.96

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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: 1.97→44.14 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 7106 5 %
Rwork0.1952 134990 -
obs0.1976 142096 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.64 Å2 / Biso mean: 34.8545 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: final / Resolution: 1.97→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13676 0 329 681 14686
Biso mean--46.18 36.47 -
Num. residues----1778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.97-1.990.36782360.30594491
1.99-2.020.34132350.27834462
2.02-2.040.34862350.26744467
2.04-2.070.28532350.25834457
2.07-2.090.29532330.24734433
2.09-2.120.28382360.24034481
2.12-2.150.31532360.23754475
2.15-2.180.31132350.23684469
2.18-2.220.29022350.23734476
2.22-2.260.31592360.22454468
2.26-2.290.25512350.21944476
2.29-2.340.27822350.21594468
2.34-2.380.27852360.21464485
2.38-2.430.27722350.2194464
2.43-2.480.27962350.21914463
2.48-2.540.27652370.20494498
2.54-2.60.23212340.18894454
2.6-2.670.24862380.1934522
2.67-2.750.25632370.19114492
2.75-2.840.26822360.19874490
2.84-2.940.24392370.20554493
2.94-3.060.27082350.20684480
3.06-3.20.28652380.2044509
3.2-3.370.24452370.20424513
3.37-3.580.23932380.19964509
3.58-3.860.22072390.18424538
3.86-4.240.21772380.16914529
4.24-4.860.19282400.15784559
4.86-6.120.20422420.17194604
6.12-8.810.17872520.15984765

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