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- PDB-8b06: TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plun... -

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Basic information

Entry
Database: PDB / ID: 8b06
TitleTRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plunger after 25 sec
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / Trytophan Synthase / Time-resolved crystallography
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
: / PYRIDOXAL-5'-PHOSPHATE / SERINE / 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: 2.49 Å
AuthorsMehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission664726European Union
CitationJournal: Nat Commun / Year: 2023
Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.
Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
History
DepositionSep 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)72,1747
Polymers71,6182
Non-polymers5565
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-64 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.789, 59.048, 67.092
Angle α, β, γ (deg.)90.000, 94.680, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-504-

CL

21B-631-

HOH

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Components

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Tryptophan synthase ... , 2 types, 2 molecules AB

#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 (bacteria)
Gene: trpA, STM1727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 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 BL21(DE3) (bacteria) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 5 types, 58 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 300, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.49→43.54 Å / Num. obs: 24816 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.095 / Rrim(I) all: 0.253 / Net I/σ(I): 6.7 / Num. measured all: 173171 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.5972.1111958427810.5420.8512.2791.299.4
8.98-43.546.50.06336735650.9970.0260.06923.498.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WSY

2wsy


Resolution: 2.49→43.54 Å / SU ML: 0.3419 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2655 1154 4.65 %
Rwork0.2281 23637 -
obs0.2298 24791 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.11 Å2
Refinement stepCycle: final / Resolution: 2.49→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 25 53 4980
Biso mean--47.75 51.23 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275043
X-RAY DIFFRACTIONf_angle_d0.52746829
X-RAY DIFFRACTIONf_chiral_restr0.0412759
X-RAY DIFFRACTIONf_plane_restr0.0038902
X-RAY DIFFRACTIONf_dihedral_angle_d9.3218703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.60.37861490.34512895X-RAY DIFFRACTION98.73
2.6-2.740.32631590.31752924X-RAY DIFFRACTION99.1
2.74-2.910.28081700.29752914X-RAY DIFFRACTION99
2.91-3.140.3181430.27462947X-RAY DIFFRACTION99.04
3.14-3.450.30391390.24892953X-RAY DIFFRACTION98.44
3.45-3.950.23621340.20622960X-RAY DIFFRACTION98.32
3.95-4.980.21931360.18132992X-RAY DIFFRACTION99.4
4.98-43.540.24261240.19863052X-RAY DIFFRACTION98.18
Refinement TLS params.Method: refined / Origin x: 65.7911186477 Å / Origin y: 17.7221800536 Å / Origin z: 15.4440755711 Å
111213212223313233
T0.342507920867 Å2-0.017593887635 Å2-0.00698664529679 Å2-0.483307374515 Å20.0110536408172 Å2--0.410214501452 Å2
L1.01589808964 °2-0.429777680175 °2-0.228998077058 °2-0.572065245997 °20.207100474426 °2--0.494864769056 °2
S0.0336394850197 Å °0.00429377165207 Å °0.0904090987172 Å °-0.0315270709967 Å °-0.00418338851268 Å °0.094439248777 Å °-0.0876226723701 Å °-0.104189565145 Å °-0.0372534298199 Å °
Refinement TLS groupSelection details: all

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