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- PDB-6usa: Crystal structure of tryptophan synthase from M. tuberculosis - a... -

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Basic information

Entry
Database: PDB / ID: 6usa
TitleCrystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK1-bound form
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/Lyase Inhibitor / PLP / HETEROTETRAMER / AMINO ACID BIOSYNTHESIS / SUBSTRATE CHANNELING / LYASE-LYASE INHIBITOR COMPLEX
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / : / MALONATE ION / Chem-P1T / DI(HYDROXYETHYL)ETHER / Chem-PZJ / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsChang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
Global Health Innovative Technology Fund United States
CitationJournal: Protein Sci. / Year: 2020
Title: Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase.
Authors: Michalska, K. / Chang, C. / Maltseva, N.I. / Jedrzejczak, R. / Robertson, G.T. / Gusovsky, F. / McCarren, P. / Schreiber, S.L. / Nag, P.P. / Joachimiak, A.
History
DepositionOct 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Advisory / Database references / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_PDB_obs_spr / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,52876
Polymers287,6568
Non-polymers5,87268
Water22,2311234
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)146,66035
Polymers143,8284
Non-polymers2,83131
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-11 kcal/mol
Surface area42190 Å2
MethodPISA
2
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,86941
Polymers143,8284
Non-polymers3,04137
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-44 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.920, 160.037, 165.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Tryptophan synthase alpha chain


Mass: 28579.449 Da / Num. of mol.: 4
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43334.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

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Non-polymers , 11 types, 1302 molecules

#3: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-PZJ / (3R,4R)-4-[4-(2-Chlorophenyl)piperazin-1-yl]-1,1-dioxothiolan-3-ol


Mass: 330.830 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H19ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1234 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% TACSIMATE, 20% PEG3350, 100 MM SODIUM MALONATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 137941 / % possible obs: 99.8 % / Redundancy: 24.9 % / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.07 / Rrim(I) all: 0.352 / Χ2: 1.132 / Net I/σ(I): 3.1 / Num. measured all: 3436417
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4420.72.17868670.6970.4992.2370.77199.9
2.44-2.4922.11.88368070.7380.4141.930.76199.9
2.49-2.5322.91.79368320.7820.3861.8350.77399.9
2.53-2.5923.31.47468360.7710.3131.5080.924100
2.59-2.6423.71.51768120.8220.321.5510.78199.9
2.64-2.723.91.31768420.8560.2751.3460.78599.7
2.7-2.7722.91.10668450.8870.2351.1310.8100
2.77-2.8523.20.98768150.9130.211.011.01899.1
2.85-2.9326.70.94468650.9470.1860.9620.83100
2.93-3.0226.90.77768550.9650.1520.7920.85599.9
3.02-3.1326.90.63168610.970.1230.6430.89699.9
3.13-3.2626.80.49468690.9830.0960.5030.94199.9
3.26-3.426.50.3768830.9880.0730.3771.02499.9
3.4-3.5825.40.28869070.990.0580.2941.1399.8
3.58-3.8124.90.21868720.9940.0440.2231.23599.6
3.81-4.127.60.17869540.9960.0340.1811.311100
4.1-4.51270.14669490.9970.0290.1491.577100
4.51-5.1625.80.12469940.9970.0250.1261.5999.9
5.16-6.4925.50.12769980.9970.0250.1291.41299.4
6.49-3025.30.08672780.9940.0180.0882.83899.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DWE

6dwe


Resolution: 2.406→29.892 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2677 1.94 %
Rwork0.1576 135134 -
obs0.1583 137811 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.73 Å2 / Biso mean: 37.5449 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: final / Resolution: 2.406→29.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19161 0 366 1234 20761
Biso mean--49.77 40.86 -
Num. residues----2602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.406-2.44970.29251340.2441650892
2.4497-2.49680.25891240.2227108100
2.4968-2.54770.23271160.21057077100
2.5477-2.60310.25981460.20347052100
2.6031-2.66360.24891300.20557139100
2.6636-2.73020.22991300.19817052100
2.7302-2.80390.24661290.1933711399
2.8039-2.88640.21061600.19397029100
2.8864-2.97950.2411420.18497102100
2.9795-3.08590.24561380.18647120100
3.0859-3.20930.23391600.17887118100
3.2093-3.35520.2081620.177086100
3.3552-3.53180.20731470.1557120100
3.5318-3.75270.17031490.13897161100
3.7527-4.04180.15471550.12797155100
4.0418-4.44730.13691490.11657207100
4.4473-5.08810.15511240.11317219100
5.0881-6.40010.17111550.1408725999
6.4001-29.8920.13041270.1357750999
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)
10.679-0.2450.24210.2665-0.04760.41280.08760.23190.0272-0.0193-0.1584-0.19930.02530.2192-0.0090.14470.00820.03570.39870.09560.395385.9928-12.857116.8128
20.4045-0.075-0.15080.4291-0.12090.66930.0302-0.0099-0.0140.0357-0.0687-0.0671-0.10820.0517-0.00050.1199-0.0147-0.0060.12360.02290.139451.0977-5.137328.5518
30.5177-0.0144-0.09390.8157-0.39930.42460.076-0.1274-0.05950.4971-0.05260.1383-0.2407-0.11480.02650.4274-0.07790.09720.2433-0.02040.20389.6186-26.898678.4323
40.1260.0852-0.23720.47230.00380.73740.0226-0.0016-0.00270.0413-0.0468-0.00830.0201-0.1039-00.1091-0.00830.0020.1690.00530.142324.0211-21.926543.7944
50.51580.15980.23080.46040.11950.5978-0.20690.2473-0.131-0.520.0969-0.15110.17070.2068-0.18130.6992-0.07680.18170.3459-0.03750.296440.8974-35.724-47.3108
60.24060.0081-0.12080.4820.07190.711-0.03880.0005-0.0169-0.1481-0.0269-0.01960.1550.0275-0.00010.17640.00750.03520.1238-0.00780.14831.4738-24.3126-12.6548
70.7921-0.52570.170.7442-0.11470.59740.1325-0.0583-0.2467-0.0355-0.06610.3616-0.0582-0.02330.01410.13640.0321-0.02220.2286-0.02020.3846-17.990113.653414.6328
80.2866-0.0669-0.21650.42980.05150.58160.0243-0.0138-0.0158-0.0819-0.03190.0301-0.0958-0.013700.1212-0.0053-0.00720.1415-0.01280.134416.39664.09812.8399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 267)A8 - 267
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 502)B5 - 502
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 267)C8 - 267
4X-RAY DIFFRACTION4(chain 'D' and resid 4 through 407)D4 - 407
5X-RAY DIFFRACTION5(chain 'E' and resid 9 through 265)E9 - 265
6X-RAY DIFFRACTION6(chain 'F' and resid 8 through 407)F8 - 407
7X-RAY DIFFRACTION7(chain 'G' and resid 9 through 267)G9 - 267
8X-RAY DIFFRACTION8(chain 'H' and resid 5 through 407)H5 - 407

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