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- PDB-1fuy: CRYSTAL STRUCTURE OF BETAA169L/BETAC170W DOUBLE MUTANT OF TRYPTOP... -

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Basic information

Entry
Database: PDB / ID: 1fuy
TitleCRYSTAL STRUCTURE OF BETAA169L/BETAC170W DOUBLE MUTANT OF TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUORO-INDOLE-PROPANOL PHOSPHATE
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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
5-FLUOROINDOLE PROPANOL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsWeyand, M. / Schlichting, I.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural basis for the impaired channeling and allosteric inter-subunit communication in the beta A169L/beta C170W mutant of tryptophan synthase.
Authors: Weyand, M. / Schlichting, I.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 21, 2021Group: Database references / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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 / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _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 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1555
Polymers71,6122
Non-polymers5433
Water3,423190
1
A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules

A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,31010
Polymers143,2234
Non-polymers1,0876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.000, 60.700, 67.400
Angle α, β, γ (deg.)90.00, 95.75, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer constructed from chain A and chain B symmetry partners are generated by the two-fold.

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Components

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TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB

#1: Protein TRYPTOPHAN SYNTHASE ALPHA CHAIN


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


Mass: 42912.832 Da / Num. of mol.: 1 / Mutation: R34S, A169L, C170W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 193 molecules

#3: Chemical ChemComp-FIP / 5-FLUOROINDOLE PROPANOL PHOSPHATE


Mass: 273.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13FNO4P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ENZYME SOLUTION: 10 MG/ML TRPS IN 50 MM BICINE PH 7.8, 1 MM EDTA, 5 MM DITHIOERYTHRITOL, 20 MUM PYRIDOXAL-5'-PHOSPHATE RESERVOI SOLUTION: 50 MM BICINE PH 7.8, 5 MM EDTA, 5 MM ...Details: ENZYME SOLUTION: 10 MG/ML TRPS IN 50 MM BICINE PH 7.8, 1 MM EDTA, 5 MM DITHIOERYTHRITOL, 20 MUM PYRIDOXAL-5'-PHOSPHATE RESERVOI SOLUTION: 50 MM BICINE PH 7.8, 5 MM EDTA, 5 MM DITHIOERYTHRITOL, 0.1 MM PYRIDOXAL-5'-PHOSPHATE, 2 MM SPERMINE, 8-12 % PEG 8000 CRYSTALLIZATION DROP CONSISTED AN INITIAL FIP CONCENTRATION OF 7 MM, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / Details: Ahmed, S.A., (1985) J. Biol. Chem., 260, 3716.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
212 %PEG80001reservoir
32 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 34995 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.4 / Biso Wilson estimate: 23.479 Å2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 1.19 % / Rmerge(I) obs: 0.295 / Num. unique all: 731 / % possible all: 37.6
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 32603 / % possible obs: 91.3 % / Num. measured all: 68906 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.35 Å / % possible obs: 92.4 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.25→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1634 -RANDOM
Rwork0.17 ---
all0.178 32603 --
obs0.178 32603 91.3 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 34 190 5187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d2.5
X-RAY DIFFRACTIONp_angle_d0.017
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d2.5

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