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- PDB-5ckv: DAHP synthase from Mycobacterium tuberculosis, fully inhibited by... -

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Basic information

Entry
Database: PDB / ID: 5ckv
TitleDAHP synthase from Mycobacterium tuberculosis, fully inhibited by tyrosine, phenylalanine, and tryptophan
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase AroG
KeywordsTRANSFERASE / TIM-barrel / shikimate pathway / feedback inhibition
Function / homology
Function and homology information


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
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHENYLALANINE / TRYPTOPHAN / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.787 Å
AuthorsMunack, S. / Krengel, U.
Funding support Norway, Switzerland, 2items
OrganizationGrant numberCountry
Research Council of Norway143645 Norway
Swiss National Science Foundation31003A-116475, 31003A-135651, and 31003A_156453 Switzerland
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 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,82521
Polymers103,7832
Non-polymers2,04219
Water73941
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
B: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
hetero molecules

A: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
B: Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,64942
Polymers207,5664
Non-polymers4,08338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area17860 Å2
ΔGint-310 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.760, 204.760, 66.774
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 , 1 types, 2 molecules AB

#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 (bacteria) / Gene: aroG, Rv2178c / Plasmid: pKTDS-HN / Production host: Escherichia coli (E. coli)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 8 types, 60 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-PHE / PHENYLALANINE


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


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: ammonium sulfate, glycerol, magnesium chloride, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.787→47.304 Å / Num. obs: 40049 / % possible obs: 99.4 % / Redundancy: 8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.9 / Num. measured all: 321302
Reflection shellResolution: 2.787→2.89 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NV8

3nv8


Resolution: 2.787→47.304 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2008 5.01 %
Rwork0.1748 --
obs0.1774 40044 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.787→47.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6916 0 126 41 7083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077180
X-RAY DIFFRACTIONf_angle_d0.7739766
X-RAY DIFFRACTIONf_dihedral_angle_d17.7544313
X-RAY DIFFRACTIONf_chiral_restr0.0451102
X-RAY DIFFRACTIONf_plane_restr0.0051283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7874-2.85710.30731050.31662504X-RAY DIFFRACTION93
2.8571-2.93430.30921710.25132714X-RAY DIFFRACTION100
2.9343-3.02060.2961410.24722705X-RAY DIFFRACTION100
3.0206-3.11810.30791400.24162701X-RAY DIFFRACTION100
3.1181-3.22950.27391780.2252668X-RAY DIFFRACTION100
3.2295-3.35880.26931490.21582744X-RAY DIFFRACTION100
3.3588-3.51160.25151240.18042733X-RAY DIFFRACTION100
3.5116-3.69670.20981610.15992696X-RAY DIFFRACTION100
3.6967-3.92820.21851420.14882740X-RAY DIFFRACTION100
3.9282-4.23130.18651260.13752725X-RAY DIFFRACTION100
4.2313-4.65680.17921470.13952735X-RAY DIFFRACTION100
4.6568-5.32980.17951200.14472762X-RAY DIFFRACTION100
5.3298-6.7120.23381610.18392770X-RAY DIFFRACTION100
6.712-47.31110.19861430.16372839X-RAY DIFFRACTION100

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