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- PDB-6xoy: Salmonella typhimurium tryptophan synthase complexed with D-trypt... -

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Basic information

Entry
Database: PDB / ID: 6xoy
TitleSalmonella typhimurium tryptophan synthase complexed with D-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 / 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 / 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
SN-GLYCEROL-1-PHOSPHATE / Chem-VB4 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 7, 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)73,02715
Polymers71,6182
Non-polymers1,41013
Water9,458525
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)146,05530
Polymers143,2354
Non-polymers2,81926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13280 Å2
ΔGint-40 kcal/mol
Surface area43720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.450, 57.720, 67.270
Angle α, β, γ (deg.)90.000, 95.466, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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-646-

HOH

21B-700-

HOH

31B-749-

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 , 5 types, 538 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 10 / 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-VB4 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan


Mass: 433.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.05 M Bicine-Na, pH 7.8, 5 mM Na2EDTA, 0.1 mM PLP, 1 mM DTT, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→36.67 Å / Num. obs: 83399 / % possible obs: 93.28 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1088 / Rrim(I) all: 0.1298 / Net I/σ(I): 6.68
Reflection shellResolution: 1.64→1.699 Å / Rmerge(I) obs: 2.02 / Mean I/σ(I) obs: 0.63 / Num. unique obs: 8135 / CC1/2: 0.218 / Rrim(I) all: 2.393

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TSY.pdb

2tsy


Resolution: 1.64→36.67 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1998 2.48 %
Rwork0.1769 78623 -
obs0.1778 80621 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 1.64→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 81 526 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145552
X-RAY DIFFRACTIONf_angle_d1.15277543
X-RAY DIFFRACTIONf_chiral_restr0.0715824
X-RAY DIFFRACTIONf_plane_restr0.0113997
X-RAY DIFFRACTIONf_dihedral_angle_d13.86582083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.50351440.47935632X-RAY DIFFRACTION94.5
1.68-1.730.46351420.43815599X-RAY DIFFRACTION93.35
1.73-1.780.40841400.38025537X-RAY DIFFRACTION92.81
1.78-1.830.33761330.31855259X-RAY DIFFRACTION88.08
1.83-1.90.26931440.26465629X-RAY DIFFRACTION94.16
1.9-1.980.25141480.22765817X-RAY DIFFRACTION95.92
1.98-2.070.22971450.18355755X-RAY DIFFRACTION96.52
2.07-2.180.22551470.16925789X-RAY DIFFRACTION96.5
2.18-2.310.21211470.16495737X-RAY DIFFRACTION95.18
2.31-2.490.2051420.15925593X-RAY DIFFRACTION93.1
2.49-2.740.22751360.16055394X-RAY DIFFRACTION89.45
2.74-3.140.2061460.15275737X-RAY DIFFRACTION95.03
3.14-3.950.15111430.13545598X-RAY DIFFRACTION92.06
3.95-36.670.18311410.15035547X-RAY DIFFRACTION89.49
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)
14.175403512342.978037604761.40309572467.478701995460.1981613102584.289559330970.3760977515980.6403220147220.534453347572-0.482838888589-0.2491985269420.659183364051-0.274165738244-0.843868977271-0.1050706817150.346147392180.2163094054060.06649258331610.5231410933250.005740308409220.418309610839-54.93334662172.9823528179620.321260279
25.03269766383-2.022490082612.376951257343.3506753248-2.266162898482.31849674130.5516339636210.4148732354010.723501527659-0.190456157014-0.296082685751-0.0899532669636-0.45321085918-0.29955300895-0.2000685255460.4567429855490.1296665547530.164239839820.3264858074580.1229677094540.442112691374-42.56870045518.8485194061421.2309901893
32.792278489232.45651032074-1.596043950954.41941878666-2.690987308745.270955675230.6006830299080.2471278934280.526220243179-0.477887576357-0.312229505482-0.598207648374-0.7773331781750.23899108342-0.2274885878170.5674661041150.1421924272640.3313893699840.4165573731410.1765232606510.726828445688-31.60155266949.4443373305818.7652205317
46.66144519097-4.63245272411-2.913397793247.683559890271.569443504771.504197323970.340187535985-0.05637810695670.7421240523450.0989588667028-0.0967943921049-0.403287028645-0.248871400996-0.101040969381-0.2234714206740.235789686543-0.01367247427380.04397195172910.2526254135840.002956686836210.257745233735-41.12497470292.8212648904329.4187620924
52.625844933910.5532980125050.9992927552444.25350338999-0.1608893118811.563049551220.1715011898860.18116055452-0.07263054451050.0367790105377-0.216257952350.2095030552130.0357235414482-0.2451010794010.06777105350280.1720759776820.02445387598510.006520214500320.31346858089-0.004753306431560.196968919796-42.862413173-9.2754143229925.9412283701
63.721560920321.248162012651.256657917463.15728284725-0.6934573126753.995780042460.3007257696471.02182604053-0.110596124685-0.704964370178-0.2674781403590.5044607121180.182003464495-0.420024353247-0.1171476611950.4272428748230.254161086449-0.09675133538530.853701226981-0.1501493638520.444483872098-49.0347986407-9.9024202927310.3657911035
73.65898748599-0.09068259209612.720285737312.72868062274-1.442522136254.070076835740.1307691468731.004301095960.101749297044-0.551108683056-0.0428007486110.363867227907-0.107738176048-0.614927701334-0.06225706362760.4564035944480.272854485899-0.0232789132881.049256019270.02001568678170.385305484007-53.5100137715-1.41342208139.16470054416
81.61028294934-1.231793682410.7212367642021.97507170025-1.150628562861.587639352410.4077446141080.4772518257750.635251946767-0.174928847403-0.241900366415-0.0641293190869-0.528770436948-0.125037287479-0.02854765798680.8714136587490.4710626486880.3229965324260.7296565704020.4619954467650.738530591202-47.270228458515.850633589712.903783043
91.19394216022-0.279901873422-0.8109595076230.2796285682160.0766043889981.732039993520.1440144076680.1989410985910.0939104560154-0.0372745767889-0.06442087461240.00702600579944-0.244203009468-0.17494342865-0.07033595214620.274943546250.00481884227847-0.03204998241060.286013215061-0.006104272771580.176151894363-14.783143141-15.02017662535.34073460147
100.9214967705650.0551889604838-0.3295887171460.2532685855630.2162408938361.313055423810.04582036932170.03130236469450.0691605977557-0.0108151195047-0.01781211898860.0219632007477-0.094444439826-0.00482986458687-0.02472438535420.205906878286-0.00542782059982-0.03408841546880.2388208083970.009781859188260.1368382321-9.02522701572-13.953920991217.9788262049
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 29 )AA2 - 291 - 28
22chain 'A' and (resid 30 through 61 )AA30 - 6129 - 60
33chain 'A' and (resid 62 through 77 )AA62 - 7761 - 76
44chain 'A' and (resid 78 through 110 )AA78 - 11077 - 109
55chain 'A' and (resid 111 through 159 )AA111 - 159110 - 158
66chain 'A' and (resid 160 through 202 )AA160 - 202159 - 201
77chain 'A' and (resid 203 through 234 )AA203 - 234202 - 233
88chain 'A' and (resid 235 through 268 )AA235 - 268234 - 267
99chain 'B' and (resid 2 through 165 )BE2 - 1651 - 164
1010chain 'B' and (resid 166 through 397 )BE166 - 397165 - 396

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