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- PDB-8rsy: TRYPTOPHAN SYNTHASE measured via serial crystallography from a ka... -

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Basic information

Entry
Database: PDB / ID: 8rsy
TitleTRYPTOPHAN SYNTHASE measured via serial crystallography from a kapton HARE-chip (50 micron)
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsLYASE / TRYPTOPHAN SYNTHASE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan metabolic process / 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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSung, S. / Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / von Stetten, D. / Mehrabi, P. / Wilmanns, M. / Schulz, E.C.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
German Research Foundation (DFG)508072649 Germany
CitationJournal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / Sung, S. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Wilmanns, M. / Schulz, E.C.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
E: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6414
Polymers71,4722
Non-polymers1682
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-56 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.600, 61.500, 67.600
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-402-

CL

21E-628-

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
Details: 1. residues from 179 to 190 are missing.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA, STM1727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42773.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1. PLP (501) - A substrate for Tryptophan synthase beta chain 2. CS (401) - A metal ion for Tryptophan synthase beta chain
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB, STM1726 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2K1, tryptophan synthase
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: PEG 300, Tris-HCl, Cesium chloride

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→91.51 Å / Num. obs: 51011 / % possible obs: 100 % / Redundancy: 43.4 % / CC1/2: 0.953 / R split: 0.23 / Net I/σ(I): 3.33
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5055 / CC1/2: 0.533 / R split: 0.951 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: HARE-chip, Kapton

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→91.51 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 2110 4.85 %
Rwork0.1904 --
obs0.1919 43500 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→91.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 26 187 5119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075065
X-RAY DIFFRACTIONf_angle_d0.8686866
X-RAY DIFFRACTIONf_dihedral_angle_d7.55709
X-RAY DIFFRACTIONf_chiral_restr0.052763
X-RAY DIFFRACTIONf_plane_restr0.005910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.29211410.29922730X-RAY DIFFRACTION100
2.16-2.210.32371260.29172732X-RAY DIFFRACTION100
2.21-2.270.28741280.27862783X-RAY DIFFRACTION100
2.27-2.340.32051530.2682721X-RAY DIFFRACTION100
2.34-2.420.30661400.24732745X-RAY DIFFRACTION100
2.42-2.50.26341400.23992736X-RAY DIFFRACTION100
2.5-2.60.32431300.23272782X-RAY DIFFRACTION100
2.6-2.720.24971220.222741X-RAY DIFFRACTION100
2.72-2.860.25981280.2112761X-RAY DIFFRACTION100
2.86-3.040.23781300.20522770X-RAY DIFFRACTION100
3.04-3.280.23311520.19132738X-RAY DIFFRACTION100
3.28-3.610.19611490.16672760X-RAY DIFFRACTION100
3.61-4.130.16381390.14582785X-RAY DIFFRACTION100
4.13-5.20.17171680.13362765X-RAY DIFFRACTION100
5.21-91.510.19291640.16532841X-RAY DIFFRACTION100

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