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- PDB-3st6: Structure of a M. tuberculosis Synthase, MbtI, in Complex with an... -

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Basic information

Entry
Database: PDB / ID: 3st6
TitleStructure of a M. tuberculosis Synthase, MbtI, in Complex with an Isochorismate Analogue Inhibitor
ComponentsIsochorismate synthase/isochorismate-pyruvate lyase mbtI
KeywordsISOMERASE/ISOMERASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / mixed alpha/beta fold / salicylate synthase / chorismate binding / ISOMERASE-ISOMERASE INHIBITOR complex
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
3-[(1-carboxyethenyl)oxy]-2-hydroxybenzoic acid / Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChi, G. / Bulloch, E.M.M. / Manos-Turvey, A. / Payne, R.J. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochemistry / Year: 2012
Title: Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis
Authors: Chi, G. / Manos-Turvey, A. / O'Connor, P.D. / Johnston, J.M. / Evans, G.L. / Baker, E.N. / Payne, R.J. / Lott, J.S. / Bulloch, E.M.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
B: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
C: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
D: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6936
Polymers195,2454
Non-polymers4482
Water18,0511002
1
A: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0352
Polymers48,8111
Non-polymers2241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0352
Polymers48,8111
Non-polymers2241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isochorismate synthase/isochorismate-pyruvate lyase mbtI


Theoretical massNumber of molelcules
Total (without water)48,8111
Polymers48,8111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Isochorismate synthase/isochorismate-pyruvate lyase mbtI


Theoretical massNumber of molelcules
Total (without water)48,8111
Polymers48,8111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.104, 115.849, 94.904
Angle α, β, γ (deg.)90.00, 91.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isochorismate synthase/isochorismate-pyruvate lyase mbtI / Mycobactin synthase protein I / Salicylate synthase mbtI


Mass: 48811.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2386c / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21:DE3
References: UniProt: Q7D785, UniProt: P9WFX1*PLUS, Lyases; Carbon-carbon lyases; Oxo-acid-lyases, isochorismate synthase
#2: Chemical ChemComp-RVE / 3-[(1-carboxyethenyl)oxy]-2-hydroxybenzoic acid


Mass: 224.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1002 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 17% PEG 6000, malic acid/KOH, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.542 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: Two Si111 Crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→29.36 Å / Num. obs: 243093 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 26.04 Å2
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 1 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G5F

2g5f


Resolution: 1.75→29.36 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9212 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 9407 5.03 %RANDOM
Rwork0.2175 ---
obs0.2188 187003 --
Displacement parametersBiso max: 121.82 Å2 / Biso mean: 32.81 Å2 / Biso min: 8.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.0499 Å20 Å2-0.9427 Å2
2---6.8846 Å20 Å2
3---4.8347 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12810 0 32 1002 13844
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4519SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes292HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2017HARMONIC5
X-RAY DIFFRACTIONt_it13203HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1748SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15950SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13203HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17954HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion16.75
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 718 5.24 %
Rwork0.2394 12973 -
all0.2401 13691 -

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