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- PDB-1bks: TRYPTOPHAN SYNTHASE (E.C.4.2.1.20) FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 1bks
TitleTRYPTOPHAN SYNTHASE (E.C.4.2.1.20) FROM SALMONELLA TYPHIMURIUM
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsLYASE / MULTIENZYME COMPLEX / TIM BARREL / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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
PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHyde, C.C.
Citation
Journal: Biochemistry / Year: 1996
Title: Exchange of K+ or Cs+ for Na+ induces local and long-range changes in the three-dimensional structure of the tryptophan synthase alpha2beta2 complex.
Authors: Rhee, S. / Parris, K.D. / Ahmed, S.A. / Miles, E.W. / Davies, D.R.
#1: 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.
#2: Journal: Bio/Technology / Year: 1990
Title: The Tryptophan Synthase Multienzyme Complex: Exploring Structure-Function Relationships with X-Ray Crystallography and Mutagenesis
Authors: Hyde, C.C. / Miles, E.W.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Tryptophan Synthase Alpha 2 Beta 2 Multienzyme Complex from Salmonella Typhimurium
Authors: Hyde, C.C. / Ahmed, S.A. / Padlan, E.A. / Miles, E.W. / Davies, D.R.
#4: Journal: J.Biol.Chem. / Year: 1985
Title: Crystallization and Preliminary X-Ray Crystallographic Data of the Tryptophan Synthase Alpha 2 Beta 2 Complex from Salmonella Typhimurium
Authors: Ahmed, S.A. / Miles, E.W. / Davies, D.R.
History
DepositionJul 10, 1998Processing site: BNL
SupersessionMar 23, 1999ID: 1WSY
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.pdbx_leaving_atom_flag / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,9584
Polymers71,6882
Non-polymers2702
Water5,260292
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9168
Polymers143,3764
Non-polymers5404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.580, 62.065, 67.610
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRYPTOPHAN SYNTHASE / TRYPTOPHAN SYNTHETASE


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE OF WILD TYPE, HOLO-ENZYME / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: TB2211 / Gene: TRPA/TRPB/TRPC / Plasmid: PSTH8 / Gene (production host): TRPA/TRPB/TRPC / Production host: Escherichia coli (E. coli) / Strain (production host): DEFICIENT IN TRP EDCBA / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE / TRYPTOPHAN SYNTHETASE


Mass: 42988.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE OF WILD TYPE, HOLO-ENZYME / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: TB2211 / Gene: TRPA/TRPB/TRPC / Plasmid: PSTH8 / Gene (production host): TRPA/TRPB/TRPC / Production host: Escherichia coli (E. coli) / Strain (production host): DEFICIENT IN TRP EDCBA / 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.8 / Details: pH 7.8

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementStarting model: 1WSY

1wsy
PDB Unreleased entry


Highest resolution: 2.2 Å
Details: THE AUTHORS OF THIS ENTRY HAVE NOT PROVIDED REFINEMENT DETAILS.
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 16 292 5214

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