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- PDB-5tch: Crystal structure of tryptophan synthase from M. tuberculosis - l... -

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Basic information

Entry
Database: PDB / ID: 5tch
TitleCrystal structure of tryptophan synthase from M. tuberculosis - ligand-free form, TrpA-G66V mutant
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / MALONATE ION / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsMichalska, K. / Maltseva, N. / Jedrzejczak, R. / Wellington, S. / Nag, P.P. / Fisher, S.L. / Schreiber, S.L. / Hung, D.T. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
Structure-guided Drug Discovery Coalition Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase.
Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / ...Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / Fisher, S.L. / Joachimiak, A. / Schreiber, S.L. / Hung, D.T.
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,47436
Polymers288,7378
Non-polymers1,73728
Water14,322795
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23718
Polymers144,3684
Non-polymers86814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-15 kcal/mol
Surface area43390 Å2
MethodPISA
2
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23718
Polymers144,3684
Non-polymers86814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-18 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.321, 158.813, 166.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase alpha chain


Mass: 28621.527 Da / Num. of mol.: 4 / Mutation: G66V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Plasmid: pMCSG81, pMCSG81-pRSF
Details (production host): pMCSG81 coexpresses TrpA and TrpB, pMCSG81-pRSF provides additional copy of TrpA
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43562.711 Da / Num. of mol.: 4 / Fragment: UNP residues 13-422
Source method: isolated from a genetically manipulated source
Details: Lys101 is attached to PLP
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: pMCSG81
Details (production host): pMCSG81 coexpresses TrpA and TrpB
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P9WFX9, tryptophan synthase
#3: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8% tacsimate pH 8.0, 20% PEG3350, cryo 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2015 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 148100 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 17
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.05 / CC1/2: 0.707 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.041 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20571 2883 1.9 %RANDOM
Rwork0.17505 ---
obs0.17565 145047 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--1.89 Å20 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19214 0 116 795 20125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01919752
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218809
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.95926806
X-RAY DIFFRACTIONr_angle_other_deg0.968343012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02752602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09922.869833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.259152936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.62115185
X-RAY DIFFRACTIONr_chiral_restr0.0770.23007
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024534
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_it0.8462.41810420
X-RAY DIFFRACTIONr_mcbond_other0.8472.41810421
X-RAY DIFFRACTIONr_mcangle_it1.463.62113018
X-RAY DIFFRACTIONr_mcangle_other1.463.62113019
X-RAY DIFFRACTIONr_scbond_it1.0782.5889332
X-RAY DIFFRACTIONr_scbond_other1.0662.5739290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8043.81113789
X-RAY DIFFRACTIONr_long_range_B_refined3.99919.63321925
X-RAY DIFFRACTIONr_long_range_B_other3.99819.62321920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.348→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 198 -
Rwork0.264 10343 -
obs--97.6 %
Refinement TLS params.

Method: refined / 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)
12.5045-0.92860.79451.7740.48341.6820.08530.25290.0156-0.14030.0215-0.29610.0550.2133-0.10680.0488-0.04380.08360.2319-0.02570.238385.3074-12.714217.1398
20.7860.0686-0.41851.18360.34191.24630.0253-0.0001-0.005-0.05460.0292-0.1645-0.04250.1616-0.05450.0212-0.01290.00950.0590.01680.041850.3337-5.906729.2324
32.10550.1448-0.15951.6512-0.49191.9530.0702-0.1087-0.16750.0331-0.06540.45570.0638-0.1761-0.00480.0357-0.00660.04980.1192-0.06690.2492-18.213813.264814.9193
40.73840.0711-0.61591.3103-0.07671.23730.0306-0.01680.03780.018-0.0080.1329-0.073-0.1232-0.02260.0133-0.00570.00950.0485-0.01490.020715.87112.72833.1369
53.05651.28270.74672.16660.48652.4231-0.52930.9784-0.1617-1.0010.4768-0.3857-0.16380.30080.05250.7246-0.23760.33460.6975-0.23910.299341.9288-36.0566-46.4245
60.82310.1534-0.6391.4774-0.47181.6038-0.0480.1429-0.157-0.2317-0.0129-0.1560.22690.02150.06090.07520.00020.0280.0501-0.04270.055831.3266-24.3555-12.0984
71.5386-0.83670.21053.2534-0.6351.9952-0.0873-0.29140.21710.80130.01510.053-0.4465-0.2160.07220.3429-0.00690.10010.1621-0.00360.17699.2315-26.698479.2437
80.99050.1722-0.53411.02610.45681.4534-0.0113-0.1327-0.0790.1362-0.01620.10130.1004-0.01650.02750.0339-0.01620.00570.04740.03090.03323.9477-22.284844.6824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 267
2X-RAY DIFFRACTION2B5 - 409
3X-RAY DIFFRACTION3G9 - 266
4X-RAY DIFFRACTION4H4 - 409
5X-RAY DIFFRACTION5E9 - 265
6X-RAY DIFFRACTION6F9 - 407
7X-RAY DIFFRACTION7C8 - 266
8X-RAY DIFFRACTION8D10 - 407

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