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- PDB-6za5: M. tuberculosis salicylate synthase MbtI in complex with salicyla... -

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Basic information

Entry
Database: PDB / ID: 6za5
TitleM. tuberculosis salicylate synthase MbtI in complex with salicylate and Mg2+
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 component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
ACETATE ION / 2-HYDROXYBENZOIC ACID / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.109 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 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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)199,72445
Polymers196,0264
Non-polymers3,69941
Water14,358797
1
A: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,74721
Polymers49,0061
Non-polymers1,74120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6498
Polymers49,0061
Non-polymers6437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3915
Polymers49,0061
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,93711
Polymers49,0061
Non-polymers93110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.973, 193.973, 257.034
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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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 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFX1, chorismate mutase, isochorismate lyase, isochorismate synthase

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Non-polymers , 5 types, 838 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.75 M MgSO4, 0.1 M MES pH 6.5

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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: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 2.109→154.831 Å / Num. obs: 131041 / % possible obs: 93.9 % / Redundancy: 27 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 2.109→2.15 Å / Redundancy: 26.5 % / Num. unique obs: 6551 / CC1/2: 0.534 / Rpim(I) all: 0.769 / % possible all: 85.6

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Processing

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

3rv7


Resolution: 2.109→154.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 6600 -RANDOM
Rwork0.195 ---
obs0.1961 131041 93.9 %-
Displacement parametersBiso mean: 52.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.2766 Å20 Å20 Å2
2--0.2766 Å20 Å2
3----0.5532 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.109→154.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13151 0 198 797 14146
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813639HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9318595HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6247SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2351HARMONIC5
X-RAY DIFFRACTIONt_it13639HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1799SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11831SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion2.45
LS refinement shellResolution: 2.11→2.13 Å
RfactorNum. reflection% reflection
Rfree0.2371 120 -
Rwork0.209 --
obs0.2103 2621 77.64 %
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)
10.8164-0.06410.0660.9740.08850.9004-0.0172-0.0958-0.0437-0.0958-0.0011-0.065-0.0437-0.0650.0183-0.29140.01040.0412-0.32980.0004-0.328842.58068.26665.2709
20.8180.02120.08230.8479-0.27291.8339-0.03490.10330.0460.10330.05620.10840.0460.1084-0.0213-0.31450.02340.0099-0.35950.0022-0.344322.979636.3814102.101
32.06310.2017-0.41861.25630.22312.09580.1080.1883-0.01920.1883-0.0980.1595-0.01920.1595-0.0099-0.2796-0.02010.0182-0.1703-0.0066-0.28967.364415.6119100.135
41.0718-0.69580.06553.1916-0.47862.1036-0.14030.53530.2050.5353-0.0126-0.15730.205-0.15730.1529-0.2593-0.09860.1229-0.46730.0082-0.329831.203580.303494.948
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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