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- PDB-6za6: M. tuberculosis salicylate synthase MbtI in complex with Ba2+ -

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Basic information

Entry
Database: PDB / ID: 6za6
TitleM. tuberculosis salicylate synthase MbtI in complex with Ba2+
ComponentsSalicylate synthase
KeywordsLYASE / salicylate / isochorismate / chorismate / mycobactins
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / 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
: / PHOSPHATE ION / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 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 / 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 1.3Jan 24, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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: Salicylate synthase
B: Salicylate synthase
C: Salicylate synthase
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,22619
Polymers196,0264
Non-polymers1,20015
Water24,3381351
1
A: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2294
Polymers49,0061
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4026
Polymers49,0061
Non-polymers3955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2294
Polymers49,0061
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3665
Polymers49,0061
Non-polymers3604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.04, 116.9, 94.09
Angle α, β, γ (deg.)90, 91.6, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Plasmid: pET28a(+)-TEV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFX1, chorismate mutase, isochorismate lyase, isochorismate synthase

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Non-polymers , 5 types, 1366 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1351 / 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: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.04 M KH2PO4, 16% PEG 8000, 16% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 1.8→43.63 Å / Num. obs: 173404 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 11664 / CC1/2: 0.622 / Rpim(I) all: 0.595

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Processing

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

3rv7


Resolution: 1.804→43.63 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 8669 -RANDOM
Rwork0.1961 ---
obs0.197 173372 99.3 %-
Displacement parametersBiso mean: 36.63 Å2
Baniso -1Baniso -2Baniso -3
1-3.1832 Å20 Å21.0729 Å2
2---7.5968 Å20 Å2
3---4.4136 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.804→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 51 1351 14630
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813539HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.918423HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6265SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2346HARMONIC5
X-RAY DIFFRACTIONt_it13539HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1793SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13149SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion2.34
LS refinement shellResolution: 1.804→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2966 173 -
Rwork0.3232 --
obs--73.63 %
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)
10.7416-0.1666-0.11930.94850.35410.83080.00110.120.02620.12-0.026-0.06360.0262-0.06360.0249-0.1372-0.0312-0.0439-0.09460.0051-0.104943.0306-8.054830.0703
20.7731-0.08760.03120.9177-0.31480.66130.0045-0.0590.0027-0.0590.0412-0.04260.0027-0.0426-0.0457-0.0961-0.0044-0.0196-0.0971-0.0315-0.13721.8673-40.612621.4167
30.9910.308-0.11960.75710.13612.28680.106-0.0492-0.3174-0.04920.0551-0.0106-0.3174-0.0106-0.1611-0.1455-0.01710.0109-0.1677-0.0222-0.1492-1.04811.211123.9149
40.8786-0.1280.24441.1664-0.46871.15420.0255-0.02560.0314-0.02560.029-0.17590.0314-0.1759-0.0545-0.1285-0.0204-0.0162-0.10510.0158-0.156648.9936-11.5504-15.7802
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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