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- PDB-8e0x: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase comple... -

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Basic information

Entry
Database: PDB / ID: 8e0x
TitleDAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
KeywordsLYASE / DAHP synthase inhibitor / DAHP oxime complex
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHOSPHOENOLPYRUVATE / PHOSPHATE ION / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBerti, P.J. / Junop, M.S. / Grainger, R.
Funding support Canada, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2017-06712 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)262034-2013 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 480432 Canada
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Canadian Institutes of Health Research (CIHR)MOP-166070 Canada
CitationJournal: Biochemistry / Year: 2022
Title: Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation.
Authors: Balachandran, N. / Grainger, R.A. / Rob, T. / Liuni, P. / Wilson, D.J. / Junop, M.S. / Berti, P.J.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,49313
Polymers152,4664
Non-polymers1,0279
Water18,1411007
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-93 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.717, 53.181, 150.366
Angle α, β, γ (deg.)90.000, 115.795, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 38116.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: aroG, b0754, JW0737 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)
References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O
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: 50.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 5 mM DAHP oxime, 5 mM phosphoenolpyruvate, 5 mM erythrose 4-pohsphate, 30% (v/v) ethylene glycol, 1:1:0.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.97→67.65 Å / Num. obs: 105376 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 17.7
Reflection shellResolution: 1.97→2.05 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5157 / CC1/2: 0.884 / Rpim(I) all: 0.254 / Rrim(I) all: 0.492 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKS

5cks


Resolution: 1.97→43.48 Å / SU ML: 0.1702 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1999 1.9 %
Rwork0.1877 103291 -
obs0.1882 105290 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.64 Å2
Refinement stepCycle: LAST / Resolution: 1.97→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10231 0 53 1007 11291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810496
X-RAY DIFFRACTIONf_angle_d1.055114257
X-RAY DIFFRACTIONf_chiral_restr0.06231641
X-RAY DIFFRACTIONf_plane_restr0.00781865
X-RAY DIFFRACTIONf_dihedral_angle_d15.30033786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.27021300.23586722X-RAY DIFFRACTION91.74
2.02-2.080.25151420.23627341X-RAY DIFFRACTION99.64
2.08-2.140.30331430.22997406X-RAY DIFFRACTION99.75
2.14-2.210.25731430.22317399X-RAY DIFFRACTION99.78
2.21-2.290.25141420.21827322X-RAY DIFFRACTION99.61
2.29-2.380.21961420.21187361X-RAY DIFFRACTION99.76
2.38-2.490.2421440.20737414X-RAY DIFFRACTION99.75
2.49-2.620.21591440.21217389X-RAY DIFFRACTION99.74
2.62-2.780.2321440.21297457X-RAY DIFFRACTION99.83
2.78-30.25431440.20657418X-RAY DIFFRACTION99.92
3-3.30.20471440.19527451X-RAY DIFFRACTION99.87
3.3-3.770.20221450.16937489X-RAY DIFFRACTION99.8
3.77-4.750.16441450.14767487X-RAY DIFFRACTION99.67
4.75-43.480.20181470.16757635X-RAY DIFFRACTION98.76

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