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

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Basic information

Entry
Database: PDB / ID: 1qop
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 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
INDOLE-3-PROPANOL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 / 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.status_code_sf / _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_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)72,0125
Polymers71,4862
Non-polymers5253
Water14,430801
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)144,02410
Polymers142,9734
Non-polymers1,0516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10930 Å2
ΔGint-57.9 kcal/mol
Surface area42990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.200, 60.300, 67.400
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOMOLECULE THE BIOLOGICALLY ACTIVE MOLECULE IS ATETRAMER OF TWO ALPHA AND TWO BETA CHAINS.

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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
Details: INHIBITOR INDOLE PROPANOL 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: 42787.688 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: P00933, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 4 types, 804 molecules

#3: Chemical ChemComp-IPL / INDOLE-3-PROPANOL PHOSPHATE


Mass: 255.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO4P
#4: 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
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
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, CRYSTALLIZATION DROP CONSISTED AN INITIAL INDOLE PROPANOLE PHOSPHATE (IPL) CONCENTRATION OF 7 MM
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.4→30.3 Å / Num. obs: 133934 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.057 / Net I/σ(I): 10.25
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.89 % / Mean I/σ(I) obs: 2.36 / Rsym value: 0.258 / % possible all: 80.8
Reflection
*PLUS
Num. measured all: 294137 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 80.8 % / Rmerge(I) obs: 0.258

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WSY

2wsy


Resolution: 1.4→20 Å / SU B: 0.91781 / SU ML: 0.03585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06129 / ESU R Free: 0.05539
Details: RESIDUES A156, A157 AND A158 WERE MODELED IN TWO CONFORMATIONS INCLUDING THE MAIN CHAIN ATOMS. THE SIDE CHAINS OF RESIDUES ILE A30, GLU A31, CYS A154, SER A178 AND GLU A254 WERE MODELED IN ...Details: RESIDUES A156, A157 AND A158 WERE MODELED IN TWO CONFORMATIONS INCLUDING THE MAIN CHAIN ATOMS. THE SIDE CHAINS OF RESIDUES ILE A30, GLU A31, CYS A154, SER A178 AND GLU A254 WERE MODELED IN TWO CONFORMATIONS THE SIDE CHAINS OF RESIDUES GLU B11, MET B22, LYS B37, LYS B50, LYS B61, ILE B65, MET B152, THR B165, LYS B219, MET B240, HIS B260, ARG B341, GLU B367 AND ARG B379 WERE MODELED IN TWO CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 6706 5 %RANDOM
Rwork0.15 ---
obs-133915 95 %-
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 0 33 801 5786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0240.05
X-RAY DIFFRACTIONp_mcbond_it3.1652
X-RAY DIFFRACTIONp_mcangle_it4.0333
X-RAY DIFFRACTIONp_scbond_it3.7982
X-RAY DIFFRACTIONp_scangle_it4.8683
X-RAY DIFFRACTIONp_plane_restr0.02120.03
X-RAY DIFFRACTIONp_chiral_restr0.1030.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.290.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1340.3
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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