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- PDB-8e0y: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase comple... -

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Basic information

Entry
Database: PDB / ID: 8e0y
TitleDAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with DAHP oxime, Pr(III), 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
DAHP Oxime / ACETATE ION / CITRATE ANION / PHOSPHATE ION / PRASEODYMIUM 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: 2.01 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)154,80719
Polymers152,4664
Non-polymers2,34115
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-113 kcal/mol
Surface area45780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.851, 53.254, 150.543
Angle α, β, γ (deg.)90.000, 115.589, 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

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Protein , 1 types, 4 molecules ABCD

#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) / Strain (production host): BL21(DE3)
References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 6 types, 660 molecules

#2: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pr / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-52L / DAHP Oxime / (2E,4R,5S,6R)-4,5,6-trihydroxy-2-(hydroxyimino)-7-(phosphonooxy)heptanoic acid


Mass: 303.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14NO10P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 50.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 1 mM Doxime, 0.1 M praseodymium(III) acetate hydrate, 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: Jan 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.01→46.47 Å / Num. obs: 98720 / % possible obs: 97.5 % / Observed criterion σ(F): 1.36 / Redundancy: 3.6 % / Biso Wilson estimate: 27.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.073 / Net I/σ(I): 12.1
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4845 / CC1/2: 0.947 / Rpim(I) all: 0.172 / Rrim(I) all: 0.33 / % possible all: 96.1

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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: 2.01→46.47 Å / SU ML: 0.2146 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 4906 4.97 %
Rwork0.2018 93790 -
obs0.2027 98696 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.11 Å2
Refinement stepCycle: LAST / Resolution: 2.01→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10146 0 88 645 10879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010410408
X-RAY DIFFRACTIONf_angle_d1.366714126
X-RAY DIFFRACTIONf_chiral_restr0.07811626
X-RAY DIFFRACTIONf_plane_restr0.00741853
X-RAY DIFFRACTIONf_dihedral_angle_d14.77593758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.30331500.25743092X-RAY DIFFRACTION96.03
2.03-2.050.2571540.25053108X-RAY DIFFRACTION96.68
2.05-2.080.30821690.24663088X-RAY DIFFRACTION98.91
2.08-2.10.29241490.2433060X-RAY DIFFRACTION96.31
2.1-2.130.27061670.23563074X-RAY DIFFRACTION96.06
2.13-2.160.25731630.23713195X-RAY DIFFRACTION99.17
2.16-2.190.27791560.22923043X-RAY DIFFRACTION96.91
2.19-2.220.23391760.23183069X-RAY DIFFRACTION96.26
2.22-2.260.27221750.22623146X-RAY DIFFRACTION99.16
2.26-2.30.26361480.2283088X-RAY DIFFRACTION96.71
2.3-2.340.28851620.22743112X-RAY DIFFRACTION97.53
2.34-2.380.29031450.23193150X-RAY DIFFRACTION99.13
2.38-2.420.25651770.22623096X-RAY DIFFRACTION95.84
2.42-2.470.25591490.22883163X-RAY DIFFRACTION99.7
2.47-2.530.24491600.21893120X-RAY DIFFRACTION96.53
2.53-2.590.21631630.22163119X-RAY DIFFRACTION98.83
2.59-2.650.24561670.22673133X-RAY DIFFRACTION97.2
2.65-2.720.23341780.22453105X-RAY DIFFRACTION98.74
2.72-2.80.24391830.22363144X-RAY DIFFRACTION97.28
2.8-2.890.21551650.22383132X-RAY DIFFRACTION99.31
2.89-30.26491440.2223164X-RAY DIFFRACTION97.38
3-3.120.22941430.21723183X-RAY DIFFRACTION98.34
3.12-3.260.20691790.20683142X-RAY DIFFRACTION98.81
3.26-3.430.20841630.19033165X-RAY DIFFRACTION98.26
3.43-3.640.19591750.183154X-RAY DIFFRACTION98.23
3.64-3.930.17831730.17383180X-RAY DIFFRACTION98.79
3.93-4.320.17151780.15653214X-RAY DIFFRACTION99.01
4.32-4.940.16071570.15513197X-RAY DIFFRACTION98.3
4.94-6.230.18321760.18633256X-RAY DIFFRACTION99.19
6.23-46.470.22661620.1942898X-RAY DIFFRACTION85.79

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