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- PDB-5cks: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase in com... -

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Basic information

Entry
Database: PDB / ID: 5cks
TitleDAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase in complex with DAHP Oxime.
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
KeywordsTransferase/transferase inhibitor / DAHP synthase / Inhibitor / Complex / Transition state mimic / Transferase-transferase inhibitor 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DAHP Oxime / beta-D-galactopyranose / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1181 Å
AuthorsBerti, P. / Junop, M. / Balachandran, N.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Canadian Institutes of Health Research (CIHR)MOP-89903 Canada
CitationJournal: Biochemistry / Year: 2016
Title: Potent Inhibition of 3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) Synthase by DAHP Oxime, a Phosphate Group Mimic.
Authors: Balachandran, N. / Heimhalt, M. / Liuni, P. / To, F. / Wilson, D.J. / Junop, M.S. / Berti, P.J.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)153,6139
Polymers152,4664
Non-polymers1,1475
Water15,006833
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-42 kcal/mol
Surface area47040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.990, 53.360, 150.655
Angle α, β, γ (deg.)90.00, 115.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-536-

HOH

DetailsTetramer confirmed by gel filtration

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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
Details: first 5 residues are unstructured in the crystal structure. Also loops 101-102 and 313-317.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: aroG, b0754, JW0737 / Plasmid: pET300 / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase
#2: 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: isolated from a genetically manipulated source
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
#3: 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.: 2 / Source method: obtained synthetically / Formula: C7H14NO10P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Mother liquor (20% PEG 3350, 200 mM trilithium citrate tetrahydrate, 6% galactose) was mixed in equal volume with DHAPS at 10 mg/ml in buffer containing 20 mM Tris-HCl, 0.1 mM TCEP.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1181→50 Å / Num. all: 85303 / Num. obs: 85303 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1181→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KFL

1kfl


Resolution: 2.1181→42.424 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1999 2.34 %Random selection
Rwork0.1808 ---
obs0.1821 85285 98.62 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.415 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.0077 Å20 Å2-1.9312 Å2
2--10.2664 Å20 Å2
3----4.2586 Å2
Refinement stepCycle: LAST / Resolution: 2.1181→42.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10367 0 74 833 11274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710615
X-RAY DIFFRACTIONf_angle_d1.02514372
X-RAY DIFFRACTIONf_dihedral_angle_d14.193918
X-RAY DIFFRACTIONf_chiral_restr0.0681656
X-RAY DIFFRACTIONf_plane_restr0.0041869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1181-2.17110.30421180.2254899X-RAY DIFFRACTION82
2.1711-2.22980.25941430.21235992X-RAY DIFFRACTION100
2.2298-2.29540.26361440.19885982X-RAY DIFFRACTION100
2.2954-2.36950.26731430.19235971X-RAY DIFFRACTION100
2.3695-2.45420.261450.19066015X-RAY DIFFRACTION100
2.4542-2.55240.25181430.19555977X-RAY DIFFRACTION100
2.5524-2.66850.28571450.20476019X-RAY DIFFRACTION100
2.6685-2.80920.28131440.20856025X-RAY DIFFRACTION100
2.8092-2.98520.2661440.20125969X-RAY DIFFRACTION100
2.9852-3.21560.25841450.19946015X-RAY DIFFRACTION100
3.2156-3.5390.2241450.18116057X-RAY DIFFRACTION100
3.539-4.05080.23351450.15936035X-RAY DIFFRACTION100
4.0508-5.10220.18351450.14196072X-RAY DIFFRACTION99
5.1022-42.43240.20461500.1676258X-RAY DIFFRACTION100

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