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- PDB-1ubs: TRYPTOPHAN SYNTHASE (E.C.4.2.1.20) WITH A MUTATION OF LYS 87->THR... -

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Basic information

Entry
Database: PDB / ID: 1ubs
TitleTRYPTOPHAN SYNTHASE (E.C.4.2.1.20) WITH A MUTATION OF LYS 87->THR IN THE B SUBUNIT AND IN THE PRESENCE OF LIGAND L-SERINE
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsLYASE/PEPTIDE / LYASE-PEPTIDE complex
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 / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRhee, S. / Parris, K. / 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: Lysine87 in the B 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.
#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 Alpha2Beta2 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 Alpha2Beta2 Complex from Salmonella Typhimurium
Authors: Ahmed, S.A. / Miles, E.W. / Davies, D.R.
History
DepositionDec 14, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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.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_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 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)72,0195
Polymers71,6442
Non-polymers3753
Water4,576254
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,03810
Polymers143,2884
Non-polymers7506
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.200, 61.800, 67.800
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 28 / 2: CIS PROLINE - PRO B 56 / 3: CIS PROLINE - PRO B 196

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein TRYPTOPHAN SYNTHASE


Mass: 28698.797 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE


Mass: 42944.965 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / Strain (production host): CB149
References: UniProt: P00933, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 4 types, 257 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Details: BOUND TO B SUBUNIT
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPLP FORMS THE EXTERNAL ALDIMINE WITH THE AMINO GROUP OF BOUND L-SERINE IN THE BETA SUBUNIT.

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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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 295 K / Method: unknown

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 19, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 56520 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
R-AXISIICPROGRAMdata collection
PROLSQrefinement
R-AXISIICdata reduction
RefinementResolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.186 50060 84.9 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4889 0 23 254 5166
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.015
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.132
X-RAY DIFFRACTIONp_mcangle_it3.243
X-RAY DIFFRACTIONp_scbond_it4.173
X-RAY DIFFRACTIONp_scangle_it6.225
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.110.1
X-RAY DIFFRACTIONp_singtor_nbd0.1930.4
X-RAY DIFFRACTIONp_multtor_nbd0.2230.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2150.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.22
X-RAY DIFFRACTIONp_staggered_tor20.315
X-RAY DIFFRACTIONp_orthonormal_tor28.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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