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- PDB-6za4: M. tuberculosis salicylate synthase MbtI in complex with 5-(3-cya... -

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Basic information

Entry
Database: PDB / ID: 6za4
TitleM. tuberculosis salicylate synthase MbtI in complex with 5-(3-cyanophenyl)furan-2-carboxylate
ComponentsSalicylate synthase
KeywordsLYASE / salicylate / isochorismate / chorismate / mycobactins
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / iron acquisition from host / isochorismate synthase / oxo-acid-lyase activity / isochorismate synthase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / iron acquisition from host / isochorismate synthase / oxo-acid-lyase activity / isochorismate synthase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / L-tryptophan biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Salicylate synthase / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(3-cyanophenyl)furan-2-carboxylic acid / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsMori, M. / Villa, S. / Meneghetti, F. / Bellinzoni, M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Shedding X-ray Light on the Role of Magnesium in the Activity ofMycobacterium tuberculosisSalicylate Synthase (MbtI) for Drug Design.
Authors: Mori, M. / Stelitano, G. / Gelain, A. / Pini, E. / Chiarelli, L.R. / Sammartino, J.C. / Poli, G. / Tuccinardi, T. / Beretta, G. / Porta, A. / Bellinzoni, M. / Villa, S. / Meneghetti, F.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 22, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _software.name
Revision 1.3Jan 24, 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: Salicylate synthase
B: Salicylate synthase
C: Salicylate synthase
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,9149
Polymers196,0264
Non-polymers8885
Water15,817878
1
A: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2553
Polymers49,0061
Non-polymers2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.336, 111.687, 94.998
Angle α, β, γ (deg.)90, 92.67, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Salicylate synthase / Chorismate mutase / CM / Isochorismate synthase/isochorismate lyase / Mycobactin synthase protein


Mass: 49006.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: mbtI, trpE2, Rv2386c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFX1, chorismate mutase, isochorismate lyase, isochorismate synthase
#2: Chemical
ChemComp-M83 / 5-(3-cyanophenyl)furan-2-carboxylic acid


Mass: 213.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Na tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.092→111.687 Å / Num. obs: 108510 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.99 / Rpim(I) all: 0.063 / Net I/σ(I): 8
Reflection shellResolution: 2.092→2.128 Å / Num. unique obs: 5396 / CC1/2: 0.803 / Rpim(I) all: 0.356

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RV7

3rv7


Resolution: 2.092→94.89 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.178
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 5425 -RANDOM
Rwork0.2082 ---
obs0.2098 108510 99.9 %-
Displacement parametersBiso mean: 43.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.7682 Å20 Å22.2624 Å2
2---8.5574 Å20 Å2
3---6.7892 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.092→94.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12651 0 65 878 13594
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812981HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8917662HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5965SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2244HARMONIC5
X-RAY DIFFRACTIONt_it12981HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1726SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11489SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion2.42
LS refinement shellResolution: 2.092→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2603 114 -
Rwork0.2359 --
obs--99.86 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7118-0.44890.12750.88580.5292.6508-0.03650.0950.01070.0950.1102-0.0310.0107-0.031-0.0737-0.2966-0.0226-0.0036-0.2028-0.0697-0.257340.5124-6.681128.7979
21.1845-0.5409-0.14441.58740.02521.10750.0469-0.0609-0.0753-0.0609-0.0283-0.0883-0.0753-0.0883-0.0186-0.2272-0.00940.0207-0.2793-0.0154-0.21531.9256-39.420720.2739
33.00811.56320.10052.44730.43762.4604-0.0975-0.0413-0.2951-0.04130.17160.0005-0.29510.0005-0.0741-0.3461-0.02860.0244-0.22940.0289-0.2348-2.681512.889722.838
41.40820.1317-0.03551.2958-0.36581.820.023-0.00290.0689-0.0029-0.0585-0.17340.0689-0.17340.0355-0.24760.0076-0.0041-0.2219-0.0285-0.220448.7209-10.0714-15.5831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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