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- PDB-8eys: X-ray crystal structure of salmonella typhimurium Tryptophan synt... -

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Basic information

Entry
Database: PDB / ID: 8eys
TitleX-ray crystal structure of salmonella typhimurium Tryptophan synthase internal aldimine at pH 5.0
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / beta-elimination / PLP-dependent
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
Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDrago, V.N. / Kovalevsky, A.Y. / Mueser, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM137008-01A1 United States
CitationJournal: Cell Rep Phys Sci / Year: 2024
Title: Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase.
Authors: Drago, V.N. / Devos, J.M. / Blakeley, M.P. / Forsyth, V.T. / Parks, J.M. / Kovalevsky, A. / Mueser, T.C.
History
DepositionOct 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain


Theoretical massNumber of molelcules
Total (without water)71,8462
Polymers71,8462
Non-polymers00
Water2,846158
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain

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


Theoretical massNumber of molelcules
Total (without water)143,6924
Polymers143,6924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8590 Å2
ΔGint-32 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.659, 61.810, 67.733
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

21B-500-

HOH

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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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 43146.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50 mM Bicine pH 7.8, 1 mM EDTA, 0.2 mM PLP, 2 mM spermine, and 6% PEG 8000; acidified with sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→29.58 Å / Num. obs: 37370 / % possible obs: 96.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.32 Å / Num. unique obs: 5337 / CC1/2: 0.906

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bks

1bks


Resolution: 2.2→16.54 Å / Cross valid method: THROUGHOUT / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 --
Rwork0.1625 69065 -
obs-37273 96.2 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.81 Å2 / Biso mean: 37.94 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 2.2→16.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 0 158 5094
Biso mean---37.19 -
Num. residues----650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.30221380.23772602274094
2.23-2.260.26271370.2262595273295
2.26-2.290.23441230.22632670279395
2.29-2.330.2761540.21722585273995
2.33-2.360.24771380.20772646278495
2.36-2.40.2321450.21362648279396
2.4-2.440.31051360.20572604274096
2.44-2.490.28521520.2092616276895
2.49-2.530.19981650.19452626279196
2.53-2.590.24291560.19072675283196
2.59-2.640.18951170.18992640275796
2.64-2.70.23831070.17922752285997
2.7-2.770.23461370.18282608274596
2.77-2.840.23781460.17852627277396
2.84-2.930.20171500.18242666281696
2.93-3.020.21661590.18162637279697
3.02-3.130.22581120.17512712282497
3.13-3.250.19361590.15932708286797
3.25-3.40.2221380.16272705284397
3.4-3.580.21521320.14772646277897
3.58-3.80.16461570.14042689284697
3.8-4.090.14391570.12892684284198
4.09-4.490.15341390.12022716285598
4.49-5.120.14811520.12362721287398
5.13-6.390.18031310.1572694282598
6.4-16.540.15261280.13442593272193

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