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- PDB-2i6y: Structure and Mechanism of Mycobacterium tuberculosis Salicylate ... -

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Basic information

Entry
Database: PDB / ID: 2i6y
TitleStructure and Mechanism of Mycobacterium tuberculosis Salicylate Synthase, MbtI
ComponentsAnthranilate synthase component I, putative
KeywordsLYASE / beta sheet
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
Salicylate synthase / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsZwahlen, J. / Subramaniapillai, K. / Zhou, R. / Kisker, C. / Tonge, P.J.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and mechanism of MbtI, the salicylate synthase from Mycobacterium tuberculosis
Authors: Zwahlen, J. / Kolappan, S. / Zhou, R. / Kisker, C. / Tonge, P.J.
History
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthranilate synthase component I, putative


Theoretical massNumber of molelcules
Total (without water)50,9511
Polymers50,9511
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.206, 143.603, 123.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Anthranilate synthase component I, putative / / PUTATIVE ISOCHORISMATE SYNTHASE / Salicylate Synthase


Mass: 50950.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mbtI, MT2454, Rv2386c / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q7D785, UniProt: P9WFX1*PLUS, anthranilate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M sodium formate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.0698, 0.9745, 0.97971
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.06981
20.97451
30.979711
Reflection

D res high: 3.2 Å / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
124.3544870.061.4614336100
223.6547290.0571.421433399.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
7.885099.410.0440.996
6.267.8810010.051.132
5.476.2610010.0541.357
4.975.4710010.0541.397
4.614.9710010.0511.454
4.344.6110010.0531.423
4.134.3410010.0591.622
3.954.1310010.0621.592
3.793.9510010.0661.638
3.663.7910010.0671.489
3.553.6610010.0761.542
3.453.5510010.0811.552
3.363.4510010.0931.538
3.273.3610010.1081.662
3.23.2710010.1041.581
7.885098.720.0420.892
6.267.8810020.0450.996
5.476.2699.920.0511.24
4.975.4710020.051.227
4.614.9710020.0491.291
4.344.6110020.0521.345
4.134.3410020.0551.468
3.954.1310020.0571.362
3.793.9510020.0621.517
3.663.7910020.0661.729
3.553.6610020.0751.7
3.453.5510020.081.714
3.363.4510020.091.67
3.273.3610020.1071.665
3.23.2710020.1041.531
ReflectionResolution: 2.5→50 Å / Num. all: 15613 / Num. obs: 15501 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Χ2: 1.253 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.560.77110091.665198.2
2.56-2.620.65110091.177199.9
2.62-2.690.44810311.278199.8
2.69-2.770.41510241.2511100
2.77-2.860.33610121.48199.8
2.86-2.960.25210351.2381100
2.96-3.080.19710281.309199.9
3.08-3.220.14610221.395199.4
3.22-3.390.11710201.772198.9
3.39-3.610.07310441.276199.8
3.61-3.880.05210281.181199.8
3.88-4.270.0410531.068199.5
4.27-4.890.03510470.996199.1
4.89-6.160.03410550.929198.3
6.16-500.02810840.821195.1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.974513.16-4.4
12 wavelength20.979710.29-9.01
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.4650.1010.0430.69
2Se52.550.0480.2030.2190.578
3Se37.4280.7660.0860.0610.471
4Se600.4320.4030.0770.526
5Se600.5930.0860.140.6
6Se600.8380.0550.0060.615
Phasing dmFOM : 0.8 / FOM acentric: 0.81 / FOM centric: 0.73 / Reflection: 7656 / Reflection acentric: 6541 / Reflection centric: 1115
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.1-19.8320.920.940.87338227111
5.7-9.10.890.910.831067841226
4.6-5.70.880.90.7812891086203
4-4.60.870.890.7312801114166
3.4-40.770.780.6822862018268
3.2-3.40.620.640.513961255141

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 34.462 / SU ML: 0.331 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.681 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 776 5 %RANDOM
Rwork0.232 ---
all0.268 15601 --
obs0.252 15469 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.915 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å20 Å2
2--2.07 Å20 Å2
3----5.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 3 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223142
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.974281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2785416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83722.283127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.94715468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9431533
X-RAY DIFFRACTIONr_chiral_restr0.1210.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022404
X-RAY DIFFRACTIONr_nbd_refined0.2550.21467
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.25
X-RAY DIFFRACTIONr_mcbond_it0.6221.52125
X-RAY DIFFRACTIONr_mcangle_it1.09423303
X-RAY DIFFRACTIONr_scbond_it1.64931131
X-RAY DIFFRACTIONr_scangle_it2.6884.5978
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 55 -
Rwork0.422 1032 -
obs-1087 97.05 %
Refinement TLS params.Method: refined / Origin x: 40.17 Å / Origin y: 48.469 Å / Origin z: 72.0486 Å
111213212223313233
T0.0841 Å20.0127 Å2-0.0422 Å2-0.072 Å20.0182 Å2---0.0313 Å2
L1.2456 °20.022 °2-0.1781 °2-2.2968 °2-1.1048 °2--2.2485 °2
S0.0399 Å °0.1782 Å °-0.0301 Å °-0.4364 Å °-0.01 Å °0.1087 Å °0.127 Å °0.0013 Å °-0.0299 Å °
Refinement TLS groupSelection: ALL

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