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- PDB-2tys: CRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA... -

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Basic information

Entry
Database: PDB / ID: 2tys
TitleCRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA2 BETA2 COMPLEX WITH LIGANDS BOUND TO THE ACTIVE SITES OF THE ALPHA AND BETA SUBUNITS REVEAL LIGAND-INDUCED CONFORMATIONAL CHANGES
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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. / Rossmann fold - #1100 / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLT / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 1.9 Å
AuthorsRhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes.
Authors: Rhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Lysine 87 in the Beta Subunit of Tryptophan Synthase that Forms an Internal Aldimine with Pyridoxal Phosphate Serves Critical Roles in Transimination, Catalysis, and Product Release
Authors: Lu, Z. / Nagata, S. / Mcphie, P. / Miles, E.W.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1164
Polymers71,6602
Non-polymers4562
Water6,449358
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2328
Polymers143,3194
Non-polymers9134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)185.800, 62.300, 67.800
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRYPTOPHAN SYNTHASE


Mass: 28698.797 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T
Source method: isolated from a genetically manipulated source
Details: L-TRYPTOPHAN BOUND TO THE BETA SUBUNIT IN A FORM OF SCHIFF BASE WITH COENZYME PYRIDOXAL 5'-PHOSPHATE
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE


Mass: 42960.922 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T
Source method: isolated from a genetically manipulated source
Details: L-TRYPTOPHAN BOUND TO THE BETA SUBUNIT IN A FORM OF SCHIFF BASE WITH COENZYME PYRIDOXAL 5'-PHOSPHATE
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / 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-PLT / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE


Mass: 433.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8
Details: 50MM NABICINE (PH 7.8), 1MM NA-EDTA, 0.8-1.5MM SPERMINE, 12% PEG8000
Crystal grow
*PLUS
Method: unknown / Details: pH is adjusted to 7.8 with NaOH
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMBicine11
21 mMNa-EDTA11
30.8-1.5 mMspermine11
412 %PEG800011

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1992
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 50490 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 3.7 / % possible all: 46.8
Reflection shell
*PLUS
% possible obs: 46.8 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Resolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.171 --
obs-49684 82.4 %
Displacement parametersBiso mean: 29.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 31 358 5323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.009
X-RAY DIFFRACTIONp_angle_d0.0180.012
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.015
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.492
X-RAY DIFFRACTIONp_mcangle_it3.233
X-RAY DIFFRACTIONp_scbond_it4.353
X-RAY DIFFRACTIONp_scangle_it6.095
X-RAY DIFFRACTIONp_plane_restr0.0120.01
X-RAY DIFFRACTIONp_chiral_restr0.0880.05
X-RAY DIFFRACTIONp_singtor_nbd0.1650.2
X-RAY DIFFRACTIONp_multtor_nbd0.1580.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.2
X-RAY DIFFRACTIONp_planar_tor2.42
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.171 / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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