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- PDB-3veh: Structure of a M. tuberculosis salicylate synthase, MbtI, in comp... -

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Basic information

Entry
Database: PDB / ID: 3veh
TitleStructure of a M. tuberculosis salicylate synthase, MbtI, in complex with an inhibitor methylAMT
ComponentsIsochorismate synthase/isochorismate-pyruvate lyase mbtI
Keywordslyase / isomerase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / salicylate synthase
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
Chem-0GA / : / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBulloch, E.M. / Chi, G. / Manos-Turvey, A. / Johnston, J.M. / Baker, E.N. / 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
DepositionJan 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Non-polymer description
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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 / _struct_ref_seq_dif.details / _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)197,09519
Polymers195,3094
Non-polymers1,78615
Water17,673981
1
A: Isochorismate synthase/isochorismate-pyruvate lyase mbtI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2164
Polymers48,8271
Non-polymers3883
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)49,2555
Polymers48,8271
Non-polymers4274
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)49,5207
Polymers48,8271
Non-polymers6936
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)49,1053
Polymers48,8271
Non-polymers2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.674, 115.955, 94.715
Angle α, β, γ (deg.)90.00, 91.59, 90.00
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
Isochorismate synthase/isochorismate-pyruvate lyase mbtI / Mycobactin synthase protein I / Salicylate synthase mbtI


Mass: 48827.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mbtI, trpE2, Rv2386c, MT2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7D785, UniProt: P9WFX1*PLUS, Lyases; Carbon-carbon lyases; Oxo-acid-lyases, isochorismate synthase

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Non-polymers , 6 types, 996 molecules

#2: Chemical
ChemComp-0GA / 3-{[(1Z)-1-carboxyprop-1-en-1-yl]oxy}-2-hydroxybenzoic acid


Mass: 238.193 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H10O6
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 291 K / pH: 8
Details: 15% PEG 4000, 0.2 M potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9543
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9543 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 127664 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.134
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.594 / Rsym value: 0.594 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.144 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6405 5 %RANDOM
Rwork0.175 ---
obs0.178 121106 99.7 %-
all-121077 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0.28 Å2
2--1.33 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13410 0 117 981 14508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01913782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9818702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81651768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20222.052614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37152224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01115178
X-RAY DIFFRACTIONr_chiral_restr0.150.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110570
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2271.58765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.087214051
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37135017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3664.54644
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 471 -
Rwork0.23 8733 -
obs--98.89 %

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