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- PDB-8eyp: Joint X-ray/neutron structure of Salmonella typhimurium tryptopha... -

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Basic information

Entry
Database: PDB / ID: 8eyp
TitleJoint X-ray/neutron structure of Salmonella typhimurium tryptophan synthase internal aldimine from microgravity-grown crystal
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / beta-elimination / PLP-dependent / alpha2beta2-tetramer
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
DEUTERATED WATER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDrago, V.N. / Kovalevsky, A. / Blakeley, M.P. / Forsyth, V.T. / 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: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation_author.identifier_ORCID / _diffrn_detector.detector

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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)71,8693
Polymers71,8462
Non-polymers231
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.510, 61.860, 67.670
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number5
Space group name H-MC121

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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 Typhi (bacteria)
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 enterica subsp. enterica serovar Typhimurium (bacteria)
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: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12891N
22891N
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.541.54
NUCLEAR REACTORILL LADI III22.85-3.8
Detector
TypeIDDetectorDate
DECTRIS EIGER R 4M1PIXELJan 27, 2020
LADI III2IMAGE PLATEJul 10, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.851
33.81
Reflection

Entry-ID: 8EYP

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.8-91.91656689330.052126.6
2.1-52.363099370.16.80.182210.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.8620.3112.4180.6
2.1-2.215.70.412252.5

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Processing

Software
NameVersionClassification
nCNS1.0.8refinement
CrysalisProdata reduction
CrysalisProdata scaling
LAUEGENdata reduction
LSCALEdata scaling
Refinement

Biso max: 100.94 Å2 / Biso mean: 46.29 Å2 / Biso min: 22.62 Å2 / % reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1BKS

1bks

/ Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)Diffraction-IDBsol (Å2)ksol (e/Å3)
1.8-29.44X-RAY DIFFRACTION0.1990.0040.182312459460706156258488.6144.08720.340369
2.1-37.6NEUTRON DIFFRACTION0.2880.010.224134125549446532689060.223000.58748
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.470.44
Luzzati d res low-5
Luzzati sigma a0.890.75
Luzzati d res high-2.1
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.210.2
Luzzati d res low-5
Luzzati sigma a0.20.18
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 1 256 5196
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg28.2
NEUTRON DIFFRACTIONx_torsion_impr_deg0.8
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg28.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.20.4741115.50.4481897NEUTRON DIFFRACTION0.0455575200836
2.2-2.310.4181295.90.4172060NEUTRON DIFFRACTION0.0375536218939.5
2.31-2.460.3921154.70.3932344NEUTRON DIFFRACTION0.0375535245944.4
2.46-2.650.4271425.20.3882581NEUTRON DIFFRACTION0.0365569272348.9
2.65-2.910.3881564.90.3653040NEUTRON DIFFRACTION0.0315574319657.3
2.91-3.330.3761794.50.3523791NEUTRON DIFFRACTION0.0285575397071.2
3.33-4.20.31124750.2924724NEUTRON DIFFRACTION0.025614497188.5
4.2-37.60.362624.90.355112NEUTRON DIFFRACTION0.0225711537494.1
1.8-1.880.2852735.40.2584791X-RAY DIFFRACTION0.0178817506457.4
1.88-1.980.2423244.70.2296519X-RAY DIFFRACTION0.0138803684377.7
1.98-2.110.23938450.2187229X-RAY DIFFRACTION0.0128766761386.8
2.11-2.270.2244345.30.2067813X-RAY DIFFRACTION0.0118808824793.6
2.27-2.50.2134164.90.2098107X-RAY DIFFRACTION0.018830852396.5
2.5-2.860.2242950.1998211X-RAY DIFFRACTION0.0118826864097.9
2.86-3.60.2034244.80.1868337X-RAY DIFFRACTION0.018854876198.9
3.6-29.440.1754404.90.1588453X-RAY DIFFRACTION0.0089005889398.8

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