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- PDB-5n2p: Sulfolobus solfataricus Tryptophan Synthase A -

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Basic information

Entry
Database: PDB / ID: 5n2p
TitleSulfolobus solfataricus Tryptophan Synthase A
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / Tryptophan Synthase
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 Å
AuthorsFleming, J. / Mayans, O.
CitationJournal: J.Mol.Biol. / Year: 2018
Title: Evolutionary Morphing of Tryptophan Synthase: Functional Mechanisms for the Enzymatic Channeling of Indole.
Authors: Fleming, J.R. / Schupfner, M. / Busch, F. / Basle, A. / Ehrmann, A. / Sterner, R. / Mayans, O.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3214
Polymers26,8971
Non-polymers4243
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-8 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.540, 76.540, 122.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 26897.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trpA, SSO0889 / Production host: Escherichia coli (E. coli) / References: UniProt: P50382, tryptophan synthase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.0, 20% [v/v] PEG 300, 5% [w/v] PEG 8000, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.059→38.27 Å / Num. obs: 22885 / % possible obs: 98 % / Redundancy: 18.9 % / Rrim(I) all: 0.068 / Net I/σ(I): 30.76
Reflection shellResolution: 2.059→2.13 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 1984 / CC1/2: 0.89 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WXJ

1wxj


Resolution: 2.059→38.27 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.2481 1132 5 %
Rwork0.2263 --
obs0.2274 22627 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.059→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 18 64 1957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051955
X-RAY DIFFRACTIONf_angle_d0.832655
X-RAY DIFFRACTIONf_dihedral_angle_d11.7471198
X-RAY DIFFRACTIONf_chiral_restr0.052315
X-RAY DIFFRACTIONf_plane_restr0.005337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.059-2.15270.40851280.39982420X-RAY DIFFRACTION90
2.1527-2.26620.49211280.41212465X-RAY DIFFRACTION91
2.2662-2.40810.32921420.28442708X-RAY DIFFRACTION100
2.4081-2.5940.32251430.25492711X-RAY DIFFRACTION100
2.594-2.8550.29351440.25072723X-RAY DIFFRACTION100
2.855-3.26790.26731440.2422739X-RAY DIFFRACTION100
3.2679-4.11650.25271460.20492782X-RAY DIFFRACTION100
4.1165-38.27660.1731570.18292947X-RAY DIFFRACTION100

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