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- PDB-7kk1: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kk1
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site and L-lysine 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
ACETATE ION / LYSINE / 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: 1.77 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 Yazd, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionOct 27, 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)209,61773
Polymers204,8536
Non-polymers4,76367
Water21,3301184
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,75922
Polymers68,2842
Non-polymers1,47520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-42 kcal/mol
Surface area22120 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13030
Polymers68,2842
Non-polymers1,84628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-25 kcal/mol
Surface area21640 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,72721
Polymers68,2842
Non-polymers1,44319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-40 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.690, 231.980, 200.450
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: 34142.234 Da / Num. of mol.: 6 / Mutation: N84A
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, 1251 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / 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.: 6 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.1 M Magnesium acetate, 12 % PEG 8000, 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: RAYONIX MX300-HS / Detector: CCD / Date: Feb 9, 2019
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→49.81 Å / Num. obs: 238163 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 9.56
Reflection shellResolution: 1.65→1.761 Å / Rmerge(I) obs: 0.7519 / Num. unique obs: 20845 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.77→49.81 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 9664 5 %
Rwork0.1682 183608 -
obs0.1697 193272 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.5 Å2 / Biso mean: 23.0355 Å2 / Biso min: 12.27 Å2
Refinement stepCycle: final / Resolution: 1.77→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13588 0 246 1184 15018
Biso mean--37.7 29.51 -
Num. residues----1783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.77-1.790.29393210.255560866407
1.79-1.810.27123180.250960496367
1.81-1.830.29223170.242560226339
1.83-1.860.29123220.229361146436
1.86-1.880.26663190.223660676386
1.88-1.910.25323220.217161126434
1.91-1.930.23613180.205460436361
1.93-1.960.22823200.198360986418
1.96-1.990.22653190.190960686387
1.99-2.030.21983180.176960496367
2.03-2.060.22543220.174661016423
2.06-2.10.22453200.179460896409
2.1-2.140.20573210.170961066427
2.14-2.180.20033190.166460486367
2.18-2.230.19133200.169160826402
2.23-2.280.20593220.173461296451
2.28-2.340.21663210.170460946415
2.34-2.40.21523200.167660816401
2.4-2.470.21173240.171661536477
2.47-2.550.19693200.162460716391
2.55-2.640.19283220.157461326454
2.64-2.750.20963230.160261386461
2.75-2.870.19433240.167561446468
2.87-3.030.20733220.172861176439
3.03-3.220.20413230.171961506473
3.22-3.460.20423250.172861726497
3.46-3.810.17473240.159461596483
3.81-4.360.15613280.140462206548
4.36-5.50.1593290.140262506579
5.5-49.810.17273410.150864646805

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