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- PDB-8e0z: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase unboun... -

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Basic information

Entry
Database: PDB / ID: 8e0z
TitleDAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase unbound:(bound)2:unbound 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 / cytosol / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)152,6088
Polymers152,4664
Non-polymers1424
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-103 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.719, 53.130, 150.200
Angle α, β, γ (deg.)90.000, 115.460, 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) / Strain (production host): BL21(DE3)
References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 50.59 %
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 DAHP oxime, 30% (v/v) ethylene glycol, 1:1:0.2, then soaked with 8 mM DAHP oxime

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→52.48 Å / Num. obs: 58010 / % possible obs: 97.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.053 / Rrim(I) all: 0.101 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4122 / CC1/2: 0.952 / Rpim(I) all: 0.111 / Rrim(I) all: 0.205 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKS

5cks


Resolution: 2.4→43.37 Å / SU ML: 0.2538 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 5122 4.86 %
Rwork0.1792 100327 -
obs0.181 58002 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10268 0 4 645 10917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910486
X-RAY DIFFRACTIONf_angle_d1.20514234
X-RAY DIFFRACTIONf_chiral_restr0.06651638
X-RAY DIFFRACTIONf_plane_restr0.00741871
X-RAY DIFFRACTIONf_dihedral_angle_d14.99173811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.22821490.20852777X-RAY DIFFRACTION76.8
2.43-2.460.30641730.20232836X-RAY DIFFRACTION79
2.46-2.490.26731720.21112880X-RAY DIFFRACTION79.21
2.49-2.520.29911290.2012968X-RAY DIFFRACTION80.13
2.52-2.550.25411710.20892905X-RAY DIFFRACTION81.87
2.55-2.590.29011610.20423056X-RAY DIFFRACTION83.6
2.59-2.620.20721530.2083060X-RAY DIFFRACTION83.78
2.62-2.660.28441560.20383130X-RAY DIFFRACTION84.76
2.66-2.70.26131810.20753161X-RAY DIFFRACTION87.42
2.7-2.750.23081380.20593232X-RAY DIFFRACTION87.94
2.75-2.790.26791390.2063246X-RAY DIFFRACTION88.43
2.79-2.850.28991550.2033252X-RAY DIFFRACTION90.37
2.85-2.90.26121710.19593319X-RAY DIFFRACTION91.24
2.9-2.960.2281700.19663441X-RAY DIFFRACTION92.12
2.96-3.020.20151810.20033371X-RAY DIFFRACTION93.84
3.02-3.090.2341520.20113465X-RAY DIFFRACTION95.11
3.09-3.170.26921750.21123549X-RAY DIFFRACTION96.28
3.17-3.260.21991810.19883534X-RAY DIFFRACTION97.12
3.26-3.350.25461980.18543565X-RAY DIFFRACTION97.59
3.35-3.460.23641900.18153528X-RAY DIFFRACTION97.66
3.46-3.580.22381790.18193590X-RAY DIFFRACTION98.02
3.58-3.730.21551780.17183587X-RAY DIFFRACTION98.74
3.73-3.90.1842030.16583621X-RAY DIFFRACTION98.84
3.9-4.10.18731630.16273634X-RAY DIFFRACTION99.27
4.1-4.360.16742110.14273587X-RAY DIFFRACTION99.14
4.36-4.70.17051850.13813627X-RAY DIFFRACTION99.63
4.7-5.170.18971710.14763649X-RAY DIFFRACTION99.45
5.17-5.910.16051830.17333644X-RAY DIFFRACTION99.48
5.91-7.440.20471580.17143635X-RAY DIFFRACTION99.61
7.45-43.370.1551960.14733478X-RAY DIFFRACTION95.5

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