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- PDB-6ouy: The crystal structure of the isolate tryptophan synthase alpha-ch... -

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Basic information

Entry
Database: PDB / ID: 6ouy
TitleThe crystal structure of the isolate tryptophan synthase alpha-chain from Salmonella enterica serovar typhimurium at 1.60 Angstrom resolution
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / tryptophan synthase / alpha-chain / wild-type / recombinant protein
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L. / Chang, C. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1350401 United States
CitationJournal: J.Biomol.Nmr / Year: 2020
Title: Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase alpha-subunit from solution-state NMR.
Authors: Sakhrani, V.V. / Hilario, E. / Caulkins, B.G. / Hatcher-Skeers, M.E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionMay 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3899
Polymers28,6991
Non-polymers6908
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-71 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.910, 70.910, 203.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: trpA, STM1727 / Variant: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pET-SUMO / Details (production host): kanamycin / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta (DE3) pLys-S / References: UniProt: P00929, tryptophan synthase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.57 Å3/Da / Density % sol: 52.15 % / Description: large diamond-like crystal
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5-2.0 M ammonium sulfate / PH range: 7.00-7.50 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryosystem / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 29, 2018 / Details: Varimax Confocal Max-Flux
RadiationMonochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→61.41 Å / Num. obs: 40745 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.078 / Rsym value: 0.07 / Net I/av σ(I): 7.2 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.694.50.6671.12593657410.3480.7560.6671.598.1
1.69-1.795.10.4441.72833355150.2170.4970.4442.4100
1.79-1.915.20.3012.32718852490.1450.3350.3013.7100
1.91-2.075.20.2382.92555948860.1120.2640.2385.8100
2.07-2.265.30.1813.62373545150.0850.20.1819.2100
2.26-2.535.30.1195.12191041410.0560.1320.11911.6100
2.53-2.925.30.0659.41938136590.0310.0720.06515.8100
2.92-3.5850.05410.61566631390.0270.060.05422.999.9
3.58-5.064.50.0319.51109924820.0160.0340.0329.699.3
5.06-19.5954.40.02223.4622414180.0120.0250.02226.796.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.364
Highest resolutionLowest resolution
Rotation19.6 Å1.93 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 40385
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.22-10033.20.901501
5.55-7.2240.30.868590
4.68-5.5529.50.938698
4.12-4.6823.60.95802
3.72-4.1224.30.94884
3.42-3.7224.10.939971
3.18-3.4222.10.9331052
2.99-3.1824.60.9161102
2.82-2.9924.80.9161166
2.68-2.8223.20.9261236
2.56-2.6822.10.9261284
2.46-2.5620.30.9371324
2.37-2.4619.40.9361369
2.28-2.3720.20.9221435
2.21-2.28200.9181448
2.14-2.2120.20.9181508
2.08-2.1419.60.9241573
2.02-2.0818.60.9351596
1.97-2.0220.50.9161644
1.92-1.9721.90.8891672
1.87-1.9220.90.8761660
1.83-1.8720.30.9141773
1.79-1.8320.10.9281806
1.75-1.7922.90.9141819
1.72-1.7522.40.9131871
1.69-1.7223.10.911909
1.66-1.6924.40.911953
1.6-1.6631.60.8623739

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Processing

Software
NameVersionClassification
CrystalClear2data collection
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.7.01phasing
DM7.0.073phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OSO

6oso


Resolution: 1.6→19.595 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.72
RfactorNum. reflection% reflection
Rfree0.2057 2006 4.97 %
Rwork0.1775 --
obs0.179 40384 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.8 Å2 / Biso mean: 30.6609 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 1.6→19.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 35 319 2296
Biso mean--63.65 41.2 -
Num. residues----258
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 (%)
1.6-1.640.32951470.27982565271295
1.64-1.68440.26881480.2382689283799
1.6844-1.73390.24741230.218427182841100
1.7339-1.78980.26471400.20152689282999
1.7898-1.85370.21631410.191327202861100
1.8537-1.92790.3051340.23622649278397
1.9279-2.01560.24871460.19642720286699
2.0156-2.12170.20671450.175727122857100
2.1217-2.25450.23721290.18782730285998
2.2545-2.42820.1971520.17242736288899
2.4282-2.6720.18411250.170628032928100
2.672-3.05740.22091530.169828112964100
3.0574-3.84730.19471730.160728323005100
3.8473-19.59680.16791500.16693004315498
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)
10.93380.25350.0770.52410.24010.5589-0.03280.0829-0.0193-0.108-0.00130.03420.01660.0745-00.2383-0.007-0.00780.16840.02360.1804-29.511513.4657-1.8052
20.7236-0.3948-0.15980.48150.41530.39820.07140.0890.05950.0304-0.08560.2331-0.0974-0.05470.00010.20560.0104-0.01770.21620.02530.2474-42.999820.3078-4.6642
30.1209-0.0164-0.02520.2977-0.08140.05330.0504-0.06080.5155-0.0025-0.01880.0281-0.2060.12220.00080.24820.0087-0.01610.28690.0130.3554-35.182133.9601-0.6092
40.63140.34120.29980.3771-0.1570.5759-0.03350.08280.0554-0.00220.0088-0.20640.03540.1228-00.199-0.0292-0.00990.23360.02280.2214-16.865221.14090.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 110 )A1 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 159 )A111 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 216 )A160 - 216
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 268 )A217 - 268

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