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- PDB-6xnc: Salmonella typhimurium tryptophan synthase complexed with L-trypt... -

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Basic information

Entry
Database: PDB / ID: 6xnc
TitleSalmonella typhimurium tryptophan synthase complexed with L-tryptophan and D-glycerol-3-phosphate
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / multi-enzyme complex / allosteric enzyme product complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / 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 / 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
SN-GLYCEROL-1-PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / TRYPTOPHAN / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPhillips, R.S.
CitationJournal: Biochemistry / Year: 2021
Title: Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase by Tryptophan and Derivatives.
Authors: Phillips, R.S. / Harris, A.P.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,45234
Polymers71,6182
Non-polymers2,83432
Water9,998555
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules

A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,90468
Polymers143,2354
Non-polymers5,66864
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)182.289, 57.529, 67.266
Angle α, β, γ (deg.)90.000, 94.830, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-719-

HOH

21B-773-

HOH

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Components

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Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpA, DD95_04145 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6FWC1, UniProt: P00929*PLUS, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 587 molecules

#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Bicine-Na, pH 7.8, 1 mM EDTA, 1 mM DTT, 0.1 mM PLP, 1 mM spermine tetrahydrochloride, 10-12% PEG 3350, 6-10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.11→34.52 Å / Num. obs: 37470 / % possible obs: 92.24 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1018 / Rrim(I) all: 0.1222 / Net I/σ(I): 9.98
Reflection shellResolution: 2.11→2.185 Å / Rmerge(I) obs: 0.4377 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 2186 / CC1/2: 0.8 / Rrim(I) all: 0.5754

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TYS.pdb

2tys


Resolution: 2.11→34.52 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 2000 5.37 %
Rwork0.1625 35215 -
obs0.1653 37215 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.5 Å2 / Biso mean: 30.9794 Å2 / Biso min: 12.37 Å2
Refinement stepCycle: final / Resolution: 2.11→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 138 555 5718
Biso mean--52.78 39.05 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025250
X-RAY DIFFRACTIONf_angle_d0.5077086
X-RAY DIFFRACTIONf_dihedral_angle_d16.2491911
X-RAY DIFFRACTIONf_chiral_restr0.04776
X-RAY DIFFRACTIONf_plane_restr0.003925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.160.3224740.2621337141149
2.16-2.220.2831070.24621840194768
2.22-2.280.34691370.22422405254288
2.28-2.360.2941480.20042540268895
2.36-2.440.27481510.19242662281397
2.44-2.540.21481510.18262654280598
2.54-2.650.25161560.17672678283498
2.65-2.790.21651370.16812687282498
2.79-2.970.21271600.17062693285399
2.97-3.20.21341550.15552731288699
3.2-3.520.21811480.14732719286799
3.52-4.020.14721620.13032725288799
4.03-5.070.18161560.12362733288999
5.07-34.520.19441580.1672811296999
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)
16.14370.54360.75042.791-0.07540.33610.02230.0558-0.13960.08240.08110.518-0.0322-0.5107-0.10640.19540.02470.04580.5654-0.03110.3054-54.98332.710721.1127
20.7928-0.635-0.03522.60810.17530.9916-0.0049-0.16830.05980.0928-0.01740.0655-0.0680.00690.02520.15850.01990.02920.3846-0.01810.2313-40.86350.636624.6888
36.24931.2187-0.26335.1803-0.70612.871-0.11810.4878-0.8115-0.41550.1560.18420.3879-0.3805-0.04520.20060.0166-0.03870.4301-0.08720.3983-49.6085-11.01511.4822
43.21531.5550.08465.939-0.03281.40190.0360.07530.1687-0.2485-0.21030.2484-0.2621-0.2940.15970.20230.08-0.00950.3644-0.01410.1887-50.83156.872811.1811
53.4448-0.7543-0.04540.8690.7081.50080.0058-0.0061-0.1950.0145-0.09540.19220.2307-0.6360.07940.1761-0.08490.00530.33830.01020.2114-30.5142-22.068314.1459
62.81020.42351.32921.08210.46993.28990.06390.2408-0.2509-0.0359-0.0081-0.01290.18810.3296-0.09730.140.00890.02820.15970.0010.1668-3.8232-26.43975.8002
70.2976-0.4078-0.22631.40550.09960.70220.0168-0.05020.1382-0.021-0.04190.10260.0018-0.0920.02290.1224-0.0219-0.00710.2869-0.00530.1303-12.5953-18.19644.992
81.6072-2.7464-0.38967.95594.2595.43450.16380.22530.3187-0.1013-0.0314-0.4796-0.1845-0.0046-0.14150.1583-0.02970.05930.31660.06540.1825-17.0218-7.20790.6973
93.6399-1.6682-3.08312.3222.8088.9380.40620.09520.3949-0.3681-0.0675-0.2742-0.55740.1341-0.34940.22570.01930.05290.18550.01850.2246-15.4815-1.15080.6668
101.5092-1.1936-0.54411.66640.14360.94050.0165-0.02280.01360.0199-0.00330.06250.0148-0.1373-0.02360.1515-0.0371-0.00230.27670.00450.1531-18.56-18.78349.924
111.6627-0.1489-0.29116.86791.62071.28740.0747-0.23990.05850.2707-0.09750.08570.0961-0.00040.03420.1166-0.0203-0.00160.29850.00140.1094-7.0115-18.665822.1527
126.0422-0.5277-0.43860.27840.2230.23020.0264-0.23510.48670.07130.11940.0086-0.04260.0497-0.14340.17360.02080.01880.3194-0.04580.2328-19.5598-5.437523.9688
130.2240.1449-0.5281.2127-0.75252.276-0.052-0.10360.10570.04770.0597-0.0616-0.00840.0816-0.0090.1167-0.0144-0.00830.2813-0.03560.1565-2.3427-13.104320.4788
140.1572-0.62840.65063.4998-1.43983.99740.04080.00940.1355-0.1029-0.1118-0.3172-0.17380.24930.09530.0465-0.00650.06210.33630.00150.21964.5526-9.089115.3218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 159 )A30 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 202 )A160 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 268 )A203 - 268
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )B2 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 70 )B38 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 113 )B71 - 113
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 141 )B114 - 141
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 165 )B142 - 165
10X-RAY DIFFRACTION10chain 'B' and (resid 166 through 220 )B166 - 220
11X-RAY DIFFRACTION11chain 'B' and (resid 221 through 269 )B221 - 269
12X-RAY DIFFRACTION12chain 'B' and (resid 270 through 301 )B270 - 301
13X-RAY DIFFRACTION13chain 'B' and (resid 302 through 364 )B302 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 397 )B365 - 397

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