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- PDB-5ckx: Non-covalent complex of DAHP synthase and chorismate mutase from ... -

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Basic information

Entry
Database: PDB / ID: 5ckx
TitleNon-covalent complex of DAHP synthase and chorismate mutase from Mycobacterium tuberculosis with bound transition state analog and feedback effectors tyrosine and phenylalanine
Components
  • Intracellular chorismate mutase
  • Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Keywordstransferase/isomerase / Protein complex / shikimate pathway / DAHP-synthase / chorismate mutase / transferase-isomerase complex
Function / homology
Function and homology information


aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process ...aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chorismate mutase, high GC Gram-positive bacteria/archaeal / DAHP synthetase, class II / Class-II DAHP synthetase family / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II ...Chorismate mutase, high GC Gram-positive bacteria/archaeal / DAHP synthetase, class II / Class-II DAHP synthetase family / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHENYLALANINE / Chem-TSA / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG / Intracellular chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMunack, S. / Okvist, M. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Remote Control by Inter-Enzyme Allostery: A Novel Paradigm for Regulation of the Shikimate Pathway.
Authors: Munack, S. / Roderer, K. / Okvist, M. / Kamarauskaite, J. / Sasso, S. / van Eerde, A. / Kast, P. / Krengel, U.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 AroG
B: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
C: Intracellular chorismate mutase
D: Intracellular chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,41227
Polymers123,9994
Non-polymers2,41323
Water70339
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
B: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
C: Intracellular chorismate mutase
D: Intracellular chorismate mutase
hetero molecules

A: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
B: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
C: Intracellular chorismate mutase
D: Intracellular chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,82454
Polymers247,9978
Non-polymers4,82646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area35690 Å2
ΔGint-508 kcal/mol
Surface area69760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.397, 203.397, 67.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Phospho-2-dehydro-3-deoxyheptonate aldolase AroG / 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: 51891.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: aroG, Rv2178c / Production host: Escherichia coli (E. coli)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase
#2: Protein Intracellular chorismate mutase / CM


Mass: 10107.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv0948c, MTCY10D7.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIC1, chorismate mutase

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Non-polymers , 8 types, 62 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#8: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#9: Chemical ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O6
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1 M Tris-HCl, pH 7.9, 0.9 M ammonium sulfate and 10% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.7→58.72 Å / Num. obs: 43154 / % possible obs: 98.5 % / Redundancy: 2.2 % / Rsym value: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
REFMACphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1A

2w1a


Resolution: 2.7→58.716 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 2173 5.04 %
Rwork0.1995 --
obs0.202 43148 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→58.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8141 0 144 39 8324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078424
X-RAY DIFFRACTIONf_angle_d0.67511410
X-RAY DIFFRACTIONf_dihedral_angle_d15.8685099
X-RAY DIFFRACTIONf_chiral_restr0.0421287
X-RAY DIFFRACTIONf_plane_restr0.0041503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.75880.3371440.27832565X-RAY DIFFRACTION100
2.7588-2.82290.31541410.27282546X-RAY DIFFRACTION99
2.8229-2.89350.32951380.27622546X-RAY DIFFRACTION99
2.8935-2.97180.33331320.26462586X-RAY DIFFRACTION100
2.9718-3.05920.27961380.25382583X-RAY DIFFRACTION100
3.0592-3.15790.30581440.25222551X-RAY DIFFRACTION99
3.1579-3.27080.33161530.23592510X-RAY DIFFRACTION98
3.2708-3.40170.29691050.23262589X-RAY DIFFRACTION98
3.4017-3.55650.26641250.22652589X-RAY DIFFRACTION99
3.5565-3.7440.24851290.19832601X-RAY DIFFRACTION99
3.744-3.97850.25421200.18232567X-RAY DIFFRACTION98
3.9785-4.28560.22691350.17092523X-RAY DIFFRACTION97
4.2856-4.71680.18421480.16272564X-RAY DIFFRACTION99
4.7168-5.39890.22281350.16672529X-RAY DIFFRACTION97
5.3989-6.80040.23851310.1962508X-RAY DIFFRACTION95
6.8004-58.72950.20151550.15942618X-RAY DIFFRACTION97

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