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- PDB-1qoq: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1qoq
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH INDOLE GLYCEROL PHOSPHATE
Components
  • TRYPTOPHAN SYNTHASE ALPHA CHAIN
  • TRYPTOPHAN SYNTHASE BETA CHAIN
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 / 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
INDOLE-3-GLYCEROL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeyand, M. / Schlichting, I.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal Structure of Wild-Type Tryptophan Synthase Complexed with the Natural Substrate Indole-3-Glycerol Phosphate.
Authors: Weyand, M. / Schlichting, I.
History
DepositionNov 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: DSSP, KABSCH & SANDER
Remark 700 SHEET DETERMINATION METHOD: DSSP, KABSCH & SANDER

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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)71,9354
Polymers71,4002
Non-polymers5342
Water9,296516
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)143,8698
Polymers142,8014
Non-polymers1,0694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10900 Å2
ΔGint-48 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.742, 60.055, 67.098
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOMOLECULE THE BIOLOGICALLY ACTIVE MOLECULE IS A TETRAMER OF TWO ALPHA AND TWO BETA CHAINS.

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Components

#1: Protein TRYPTOPHAN SYNTHASE ALPHA CHAIN


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NATURAL SUBSTRATE INDOLE GLYCEROL PHOSPHATE BOUND TO THE ALPHA SITE
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Gene: TRPA / Plasmid: PSTB7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE BETA CHAIN


Mass: 42701.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Gene: TRPB / Plasmid: PSTB7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase
#3: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#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.: 516 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growMethod: 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, RESERVOIR 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, RESERVOIR 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, HANGING DROP GEOMETRY IN CONTRAST TO WHAT HAS BEEN IMPLICATED IN THE PUBLICATION ASSOCIATED WITH THIS PDB-ENTRY (WEYAND & SCHLICHTING, BIOCHEMISTRY 38: 16469-16480, (1999)), THE PH OF THE COMPLEX WAS NOT NEUTRAL BUT 5.0-5.2. THEREFORE, THE STRUCTURE WAS RE-DETERMINED AT PH 7.0 (PDB CODE 2RHG) AND ALSO AT PH 9.0 (PDB CODE 2RH9). THIS DATA SHOWS THAT CLOSURE OF LOOP ALPHA-L6 IS CAUSED BY THE LOW PH AND NOT BY BINDING OF IGP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMBicine1drop
310 mMNa EDTA1drop
41 mMdi-thioerythritol1drop
50.020 mMPLP1drop
650 mMBicine1reservoir
75 mMdi-thioerythritol1reservoir
85 mMNa EDTA1reservoir
90.1 mMPLP1reservoir
102 mMspermine1reservoir
112 mM1reservoirNaN3
128-12 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 1998
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→31.2 Å / Num. obs: 63674 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 3.49 % / Rsym value: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.57 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.21 / % possible all: 70.8
Reflection
*PLUS
Num. measured all: 219018 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 70.8 % / Rmerge(I) obs: 0.209

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOP

1qop


Resolution: 1.8→20 Å / SU B: 2.51 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.12
Details: THE SIDE CHAINS OF RESIDUES GLU A49, CYS B170, GLU B182 AND MET B240 WERE MODELED IN TWO CONFORMATIONS GLY B 395: THE C-TERMINAL RESIDUES GLU B396 AND ILE B397 WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3126 5 %RANDOM
Rwork0.171 ---
obs-63650 94 %-
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 34 516 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5372
X-RAY DIFFRACTIONp_mcangle_it2.1283
X-RAY DIFFRACTIONp_scbond_it2.2152
X-RAY DIFFRACTIONp_scangle_it3.3513
X-RAY DIFFRACTIONp_plane_restr0.02540.03
X-RAY DIFFRACTIONp_chiral_restr0.1540.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2590.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.220
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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