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- PDB-6u6c: Crystal structure of tryptophan synthase from M. tuberculosis - a... -

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Basic information

Entry
Database: PDB / ID: 6u6c
TitleCrystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK2-bound form
Components(Tryptophan synthase ...) x 2
KeywordsLyase/Lyase Inhibitor / PLP / HETEROTETRAMER / AMINO ACID BIOSYNTHESIS / SUBSTRATE CHANNELING / LYASE-LYASE INHIBITOR COMPLEX / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / plasma membrane / cytoplasm / cytosol
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 / 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. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / ALANINE / FORMIC ACID / : / MALONATE ION / Chem-P1T / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-PZV / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 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
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
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)299,001163
Polymers287,6568
Non-polymers11,345155
Water21,5281195
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)149,11278
Polymers143,8284
Non-polymers5,28474
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21190 Å2
ΔGint22 kcal/mol
Surface area41530 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)149,88985
Polymers143,8284
Non-polymers6,06181
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint33 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.106, 159.226, 164.973
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 , 13 types, 1350 molecules

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


Mass: 46.025 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical
ChemComp-PZV / 1-(2-fluorobenzene-1-carbonyl)-N-methyl-2,3-dihydro-1H-indole-5-sulfonamide


Mass: 334.365 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#8: 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 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#11: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#12: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#13: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1195 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M sodium malonate, 20% PEG3350

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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: 138216 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.089 / Rrim(I) all: 0.321 / Χ2: 0.891 / Net I/σ(I): 3 / Num. measured all: 1758336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4410.71.64968450.6610.5271.7330.75499.7
2.44-2.4911.41.50768760.7090.4641.5780.7799.9
2.49-2.5311.91.41468290.7510.4251.4780.7499.9
2.53-2.5912.31.28168240.7720.3761.3360.81299.8
2.59-2.6412.61.23868740.8020.361.290.74999.9
2.64-2.712.61.14368800.8310.3311.1910.74999.9
2.7-2.7712.30.95668360.8590.280.9970.75599.8
2.77-2.8511.80.82468250.8570.2480.8620.86899.2
2.85-2.9313.70.78268710.9330.2170.8120.77799.8
2.93-3.0213.60.6568880.950.180.6750.77299.8
3.02-3.1313.60.51768950.9620.1440.5370.78299.8
3.13-3.2613.50.40468740.9750.1130.420.793100
3.26-3.413.30.30868960.9830.0870.320.82399.8
3.4-3.5812.80.23569280.9880.0680.2450.85199.9
3.58-3.8112.40.17668710.9920.0510.1840.89898.9
3.81-4.113.90.14769590.9940.0410.1520.98499.8
4.1-4.5113.60.11469420.9960.0320.1181.04199.7
4.51-5.16130.10269940.9960.0290.1061.04299.7
5.16-6.4912.70.11770150.9940.0340.1221.13799.1
6.49-3012.60.06772940.9950.020.071.61599.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DWE

6dwe


Resolution: 2.402→29.876 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1951 2691 1.95 %
Rwork0.1529 --
obs0.1537 138098 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.74 Å2 / Biso mean: 31.1161 Å2 / Biso min: 4.77 Å2
Refinement stepCycle: final / Resolution: 2.402→29.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19188 0 732 1195 21115
Biso mean--50.21 36.5 -
Num. residues----2609
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.402-2.44540.24971450.222683397
2.4454-2.49240.27281220.20957143100
2.4924-2.54330.27171210.20387068100
2.5433-2.59850.2721420.19797061100
2.5985-2.6590.23941360.19657128100
2.659-2.72540.2611270.19197085100
2.7254-2.7990.26411330.19117068100
2.799-2.88130.22411580.1827070100
2.8813-2.97430.22881350.17977089100
2.9743-3.08050.23151450.17477110100
3.0805-3.20370.24931580.1747122100
3.2037-3.34930.20911640.15987089100
3.3493-3.52560.19421480.14597142100
3.5256-3.74610.16331500.135709799
3.7461-4.03470.16611540.12287150100
4.0347-4.43960.1551480.1127198100
4.4396-5.07930.13121240.1087213100
5.0793-6.3890.16151540.1381723699
6.389-29.8760.14071270.1364750599
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)
10.0013-0.0006-0.00030.0016-0.00110.001-0.0090.00910.0022-0.0231-0.0084-0.0231-0.00040.0029-00.21720.07990.05950.37770.02950.321594.9542-12.24644.6167
20.0195-0.01350.02010.0172-0.01430.01790.05840.0197-0.01770.0394-0.0057-0.07640.00990.005300.0961-0.0073-0.00340.15860.02350.23787.7558-13.790125.66
30.00860.0080.0020.00630.00020.0039-0.02270.04950.0380.02030.0154-0.0374-0.03860.05500.0902-0.02680.01450.16650.0290.250287.3285-1.6721.1298
40.0134-0.00660.00710.00770.00130.00980.06840.13060.00240.0062-0.0217-0.09690.0275-0.0196-00.14640.01780.03360.27010.04180.224679.2346-8.2648.9292
50.00080.00190.00190.00420.00430.00380.00740.132-0.10240.0104-0.0366-0.01370.0364-0.003700.18570.0390.00140.2663-0.09580.297684.1824-24.41938.158
60.004-0.00630.0010.0068-0.00120.0003-0.01640.0516-0.0710.0305-0.0636-0.03140.04610.032100.16530.04730.00170.19670.00380.363693.2899-23.954421.0107
70.0010.0013-0.00230.0003-0.00230.00990.04390.03490.0026-0.02870.0278-0.0157-0.0193-0.0034-00.18980.01930.0350.22130.05790.194558.6190.429912.485
80.00380.00370.00730.00620.00910.01420.04530.02660.0063-0.03760.03350.0391-0.03460.0142-00.10720.00270.00560.1370.00880.105647.5629-12.88811.6568
90.03240.0371-0.04490.0833-0.03880.0650.0490.0032-0.0007-0.0248-0.0487-0.0116-0.0227-0.00020.00080.08110.00680.00850.08660.00480.085449.1053-9.578927.8302
100.05460.011-0.02280.04120.04290.04680.0356-0.03220.01020.0236-0.0047-0.0412-0.08690.004800.0869-0.00870.00730.08550.00530.074653.89942.444136.3558
110.02560.00840.01310.0394-0.0360.05080.0116-0.07560.01660.0862-0.0430.0565-0.0477-0.0414-0.05520.3937-0.00350.19860.2645-0.04130.21245.3439-27.466185.1029
120.0184-0.0115-0.00540.11340.00830.00320.0201-0.0383-0.03550.2332-0.03950.1254-0.0527-0.0018-0.01430.2105-0.12410.13250.11630.03220.144712.3114-33.86974.2994
130.0704-0.01740.03240.04790.00240.01780.0199-0.0388-0.04160.02780.0070.0776-0.0896-0.03340.05080.2192-0.01640.14910.1959-0.0240.24891.5514-21.51770.5498
140.0518-0.01920.00790.03690.00470.00330.0975-0.10820.06150.2126-0.02470.0206-0.0341-0.02120.06860.5448-0.07290.13380.2004-0.09070.156912.363-19.243386.4745
150.00530.00520.0070.0938-0.03030.0320.05120.0541-0.01560.0449-0.03450.0678-0.0255-0.09060.00180.0516-0.01020.03330.1829-0.01850.15078.2986-15.771649.9165
160.09490.0649-0.05190.1252-0.03570.16020.0110.0075-0.00760.0287-0.0293-0.01180.0334-0.0400.0695-0.01410.0070.08650.00490.090926.2639-22.566842.8421
170.0880.07910.05240.17170.0520.1118-0.21540.1515-0.1119-0.28880.0718-0.07540.1835-0.026-0.26480.4959-0.08580.2030.1789-0.11010.082137.3395-40.0792-45.9691
180.00990.00380.00350.0040.00230.009-0.08510.0088-0.0219-0.0359-0.0435-0.03150.03540.0416-0.00010.38460.00270.1760.28140.00450.334351.0867-35.3921-39.8443
190.0536-0.00560.00020.0042-0.00260.002-0.00750.09660.0127-0.18980.0205-0.04190.040.04590.02420.5474-0.16930.10550.34530.02940.127842.2525-27.8653-55.5499
200.08550.0174-0.18520.0087-0.03820.446-0.00560.00050.00110.0020.00690.0024-0.00310.001500.5845-0.03010.02260.5843-0.01130.566341.2603-26.4798-55.72
210.01090.00360.00640.0070.00390.0028-0.0421-0.0038-0.0033-0.06060.0528-0.05590.08030.099-00.14830.03470.05050.1820.01250.180248.4784-26.6005-19.4006
220.0857-0.096-0.06410.12750.06110.1599-0.0425-0.0062-0.0109-0.0513-0-0.00530.0782-0.0387-0.00060.0801-0.01640.0150.053-0.0120.064729.5668-23.7787-11.9911
230.0207-0.00590.02330.0793-0.03190.03580.0970.0012-0.0226-0.0348-0.01260.18750.0412-0.04550.00730.09640.0223-0.00470.1669-0.02230.2254-20.843514.26349.6404
240.00260.00010.00020.00580.00290.00440.03940.03050.0091-0.0019-0.0170.0277-0.02140.0267-00.13580.03240.02580.1533-0.00580.1842-14.113223.759610.4572
250.0102-0.0012-0.01070.0053-0.00320.0132-0.0044-0.082-0.05480.02250.02920.0554-0.02160.0509-00.1559-0.00060.0340.168-0.00430.1752-9.499514.40222.3958
260.02510.0009-0.01240.0094-0.00760.0085-0.0342-0.0894-0.1286-0.0126-0.02540.21950.0397-0.0191-0.00050.141-0.0223-0.00840.1760.04430.3277-25.57574.817516.9922
270.0011-0.00220.0010.0065-0.00120.00350.0373-0.0289-0.0206-0.00570.0490.0196-0.0150.036800.1782-0.0130.01240.2359-0.03040.174312.817913.307317.9604
280.098-0.0329-0.07630.17630.03410.13520.0322-0.012-0.0151-0.0323-0.03270.005-0.0489-0.0161-00.0605-0.00270.00190.0742-0.01260.058816.56583.31611.55
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 21 )A8 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 85 )A22 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 126 )A86 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 197 )A127 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 231 )A198 - 231
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 267 )A232 - 267
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 31 )B4 - 31
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 64 )B32 - 64
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 258 )B65 - 258
10X-RAY DIFFRACTION10chain 'B' and (resid 259 through 408 )B259 - 408
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 37 )C8 - 37
12X-RAY DIFFRACTION12chain 'C' and (resid 38 through 142 )C38 - 142
13X-RAY DIFFRACTION13chain 'C' and (resid 143 through 197 )C143 - 197
14X-RAY DIFFRACTION14chain 'C' and (resid 198 through 267 )C198 - 267
15X-RAY DIFFRACTION15chain 'D' and (resid 4 through 50 )D4 - 50
16X-RAY DIFFRACTION16chain 'D' and (resid 51 through 407 )D51 - 407
17X-RAY DIFFRACTION17chain 'E' and (resid 9 through 142 )E9 - 142
18X-RAY DIFFRACTION18chain 'E' and (resid 143 through 197 )E143 - 197
19X-RAY DIFFRACTION19chain 'E' and (resid 198 through 265 )E198 - 265
20X-RAY DIFFRACTION20chain 'E' and (resid 266 through 266 )E301
21X-RAY DIFFRACTION21chain 'F' and (resid 4 through 50 )F4 - 50
22X-RAY DIFFRACTION22chain 'F' and (resid 51 through 407 )F51 - 407
23X-RAY DIFFRACTION23chain 'G' and (resid 8 through 85 )G8 - 85
24X-RAY DIFFRACTION24chain 'G' and (resid 86 through 126 )G86 - 126
25X-RAY DIFFRACTION25chain 'G' and (resid 127 through 197 )G127 - 197
26X-RAY DIFFRACTION26chain 'G' and (resid 198 through 267 )G198 - 267
27X-RAY DIFFRACTION27chain 'H' and (resid 4 through 31 )H4 - 31
28X-RAY DIFFRACTION28chain 'H' and (resid 32 through 407 )H32 - 407

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