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- PDB-3rv8: Structure of a M. tuberculosis Salicylate Synthase, MbtI, in Comp... -

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Basic information

Entry
Database: PDB / ID: 3rv8
TitleStructure of a M. tuberculosis Salicylate Synthase, MbtI, in Complex with an Inhibitor with Cyclopropyl R-Group
ComponentsIsochorismate synthase/isochorismate-pyruvate lyase mbtI
KeywordsISOMERASE/ISOMERASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / 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
Chem-RVC / Chem-VCE / Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 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
DepositionMay 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Non-polymer description
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)196,5669
Polymers195,2454
Non-polymers1,3215
Water5,729318
1
A: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0752
Polymers48,8111
Non-polymers2641
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)49,0752
Polymers48,8111
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3403
Polymers48,8111
Non-polymers5282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0752
Polymers48,8111
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.152, 115.939, 95.852
Angle α, β, γ (deg.)90.00, 91.44, 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-RVC / 3-{[(Z)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid


Mass: 264.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12O6
#3: Chemical ChemComp-VCE / 3-{[(E)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid


Mass: 264.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IN CHAIN C HAS BOTH ISOMERS MODELLED IN WITH 0.5 OCCUPANCY FOR EACH.

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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: 50.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16% PEG 6000, 0.2M Malic acid/KOH, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 27, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→19.73 Å / Num. obs: 84681 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 41.64 Å2
Reflection shellResolution: 2.29→2.41 Å / Mean I/σ(I) obs: 1.9 / % possible all: 91.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→19.73 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.8937 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 4239 5.01 %RANDOM
Rwork0.1994 ---
all0.201 84652 --
obs0.201 84652 --
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 42.34 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.1158 Å20 Å2-1.0114 Å2
2---11.3619 Å20 Å2
3---9.2461 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.29→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 0 95 318 13147
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4407SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes303HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2002HARMONIC5
X-RAY DIFFRACTIONt_it13067HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1736SEMIHARMONIC5
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_contact14843SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13067HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17780HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.11
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2465 262 4.81 %
Rwork0.2365 5190 -
all0.237 5452 -

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