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

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Basic information

Entry
Database: PDB / ID: 8ezc
TitleX-ray crystal structure of salmonella typhimurium Tryptophan synthase internal aldimine
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 / 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
Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDrago, V.N. / 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 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8693
Polymers71,8462
Non-polymers231
Water7,602422
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)143,7386
Polymers143,6924
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8760 Å2
ΔGint-53 kcal/mol
Surface area45010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.549, 58.820, 67.290
Angle α, β, γ (deg.)90.000, 94.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-647-

HOH

21B-782-

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: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 7.8
Details: 50 mM Bicine pH 7.8, 1 mM EDTA, 0.2 mM PLP, 2 mM spermine, and 6-8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→39.49 Å / Num. obs: 94632 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.69 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 13710 / Rpim(I) all: 0.631

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Processing

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

1bks


Resolution: 1.6→36.841 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 5320 2.88 %
Rwork0.195 179377 -
obs0.1953 94609 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.65 Å2 / Biso mean: 27.2851 Å2 / Biso min: 8.85 Å2
Refinement stepCycle: final / Resolution: 1.6→36.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 1 422 5359
Biso mean--19.42 33.05 -
Num. residues----650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.36311740.32835906608098
1.62-1.640.32911680.32556004617298
1.64-1.660.27751610.30615876603798
1.66-1.680.3271760.29295926610298
1.68-1.70.30891970.28355890608798
1.7-1.720.27151700.26735975614598
1.72-1.750.28581670.26315911607899
1.75-1.770.28281620.25845983614599
1.77-1.80.251680.2455920608899
1.8-1.830.24591770.23475978615599
1.83-1.860.2521730.22975943611699
1.86-1.90.20661910.23155984617599
1.9-1.930.24651720.22465951612399
1.93-1.970.25461520.22096039619199
1.97-2.020.24741800.20225918609899
2.02-2.060.25351510.20486044619599
2.06-2.110.2391450.192459976142100
2.11-2.170.20461920.185460346226100
2.17-2.240.20051930.18459536146100
2.24-2.310.19121980.187760386236100
2.31-2.390.18141960.181759176113100
2.39-2.490.18281850.185560856270100
2.49-2.60.21781510.182160066157100
2.6-2.740.16891640.179460246188100
2.74-2.910.15881920.183760506242100
2.91-3.130.20491830.18360436226100
3.13-3.450.18021900.172360096199100
3.45-3.940.1921960.164559896185100
3.94-4.970.13941760.160360296205100
4.97-36.840.18512200.182559556175100

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