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- PDB-4qys: TrpB2 enzymes -

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Basic information

Entry
Database: PDB / ID: 4qys
TitleTrpB2 enzymes
ComponentsTryptophan synthase beta chain 2
KeywordsLYASE / Enzyme evolution / functional annotation / tryptophan synthase
Function / homology
Function and homology information


L-serine hydro-lyase (adding indole, L-tryptophan-forming) activity / tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Tryptophan synthase, beta chain-like / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold ...Tryptophan synthase, beta chain-like / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-PLR / PHOSPHOSERINE / Tryptophan synthase beta chain 2
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsBusch, F. / Rajendran, C. / Loeffler, P. / Merkl, R. / Sterner, R.
CitationJournal: Biochemistry / Year: 2014
Title: TrpB2 enzymes are O-phospho-l-serine dependent tryptophan synthases
Authors: Busch, F. / Rajendran, C. / Mayans, O. / Loffler, P. / Merkl, R. / Sterner, R.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tryptophan synthase beta chain 2
A: Tryptophan synthase beta chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3955
Polymers98,7292
Non-polymers6653
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-20 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.564, 61.903, 109.574
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan synthase beta chain 2


Mass: 49364.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Gene: trpB2, SSO1145 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q97TX6, tryptophan synthase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.438 Å / Num. obs: 52794 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1589) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.939→46.438 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2641 5 %
Rwork0.1946 --
obs0.1975 52792 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.939→46.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 41 216 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086660
X-RAY DIFFRACTIONf_angle_d1.0889026
X-RAY DIFFRACTIONf_dihedral_angle_d13.8972490
X-RAY DIFFRACTIONf_chiral_restr0.041977
X-RAY DIFFRACTIONf_plane_restr0.0051144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9389-1.97410.3395950.3045181267
1.9741-2.01210.31151390.2908263898
2.0121-2.05320.37871410.2767267398
2.0532-2.09780.25531410.2388266998
2.0978-2.14660.27761430.2183272799
2.1466-2.20030.2791420.2108270099
2.2003-2.25980.2681430.20722716100
2.2598-2.32630.24351440.19922723100
2.3263-2.40140.26521430.20072727100
2.4014-2.48720.25951430.19522705100
2.4872-2.58670.27921430.20832731100
2.5867-2.70450.28141440.21362719100
2.7045-2.8470.2811430.2149271799
2.847-3.02540.25141410.2118269098
3.0254-3.25890.2521410.2064267697
3.2589-3.58680.29071350.1947255993
3.5868-4.10550.22041370.1678261194
4.1055-5.17140.22461410.1586268296
5.1714-46.45140.21871420.178267694

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