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- PDB-8e0v: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase comple... -

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Basic information

Entry
Database: PDB / ID: 8e0v
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 / 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
beta-D-galactopyranose / : / 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: 2.3 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)153,75215
Polymers152,4664
Non-polymers1,28611
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15430 Å2
ΔGint-82 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.193, 52.908, 150.481
Angle α, β, γ (deg.)90.000, 115.711, 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 / Sugars , 2 types, 7 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
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 933 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
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 erythrose 4-phosphate, 5 mM phosphoenolpyruvate, 30% (w/v) D-(+)-galactose

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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: 2.3→64.45 Å / Num. obs: 66903 / % possible obs: 96.1 % / Observed criterion σ(F): 1.35 / Redundancy: 3.7 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4452 / CC1/2: 0.883 / Rpim(I) all: 0.241 / Rrim(I) all: 0.461 / % 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: 2.3→49.65 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 1991 2.98 %
Rwork0.1943 64775 -
obs0.1953 66766 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10228 0 70 925 11223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012310475
X-RAY DIFFRACTIONf_angle_d1.351314221
X-RAY DIFFRACTIONf_chiral_restr0.07141648
X-RAY DIFFRACTIONf_plane_restr0.00871859
X-RAY DIFFRACTIONf_dihedral_angle_d15.24373805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.25791410.24714573X-RAY DIFFRACTION99.37
2.36-2.420.26361380.24414577X-RAY DIFFRACTION99.62
2.42-2.490.28891410.23834549X-RAY DIFFRACTION99.68
2.49-2.570.28481420.23314604X-RAY DIFFRACTION99.56
2.57-2.660.27611410.24594591X-RAY DIFFRACTION99.6
2.66-2.770.28711420.23944602X-RAY DIFFRACTION99.58
2.77-2.90.29341400.22774565X-RAY DIFFRACTION99.64
2.9-3.050.24171420.2144602X-RAY DIFFRACTION99.71
3.05-3.240.27631420.20444626X-RAY DIFFRACTION99.77
3.24-3.490.19991430.18634647X-RAY DIFFRACTION99.83
3.49-3.840.21271420.16624639X-RAY DIFFRACTION99.85
3.84-4.40.16211450.15194682X-RAY DIFFRACTION99.83
4.4-5.540.20141420.16024669X-RAY DIFFRACTION99.69
5.54-49.650.17741500.16954849X-RAY DIFFRACTION99.86

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