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- PDB-3pr2: Tryptophan synthase indoline quinonoid structure with F9 inhibito... -

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Basic information

Entry
Database: PDB / ID: 3pr2
TitleTryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / alpha-beta barrel / TIM-barrel / tryptophan synthesis
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
Chem-7MN / : / Chem-F9F / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsLai, J. / Niks, D. / Wang, Y. / Domratcheva, T. / Barends, T.R.M. / Schwarz, F. / Olsen, R.A. / Elliott, D.W. / Fatmi, M.Q. / Chang, C.A. ...Lai, J. / Niks, D. / Wang, Y. / Domratcheva, T. / Barends, T.R.M. / Schwarz, F. / Olsen, R.A. / Elliott, D.W. / Fatmi, M.Q. / Chang, C.A. / Schlichting, I. / Dunn, M.F. / Mueller, L.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase.
Authors: Lai, J. / Niks, D. / Wang, Y. / Domratcheva, T. / Barends, T.R. / Schwarz, F. / Olsen, R.A. / Elliott, D.W. / Fatmi, M.Q. / Chang, C.E. / Schlichting, I. / Dunn, M.F. / Mueller, L.J.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_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

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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)71,9277
Polymers70,7272
Non-polymers1,2005
Water5,152286
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)143,85414
Polymers141,4534
Non-polymers2,40110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10020 Å2
ΔGint-33 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.170, 60.620, 67.380
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1-

CS

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Components

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Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28496.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1727, 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: 42230.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1726, trpB / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 291 molecules

#3: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS
#4: Chemical ChemComp-7MN / (Z)-N-[(1E)-1-carboxy-2-(2,3-dihydro-1H-indol-1-yl)ethylidene]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methanaminium


Type: peptide linking / Mass: 436.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N3O7P
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 MM BICINE, 1 MM EDTA, 5 MM DITHIOERYTHRITOL, 0.02 MM PYRIDOXAL PHOSPHATE SOLUTION, 2 MM SPERMINE, AND 10% PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 59360 / Num. obs: 59360 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.95 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CNSrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→19.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22712 3122 5 %RANDOM
Rwork0.19806 ---
obs0.19953 59360 100 %-
all-59360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.466 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20.14 Å2
2--5.05 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 55 286 5305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225116
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9826933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77724.155219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3691532
X-RAY DIFFRACTIONr_chiral_restr0.080.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023894
X-RAY DIFFRACTIONr_nbd_refined0.1790.32575
X-RAY DIFFRACTIONr_nbtor_refined0.3040.53536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5608
X-RAY DIFFRACTIONr_metal_ion_refined0.3750.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.515
X-RAY DIFFRACTIONr_mcbond_it0.4631.53262
X-RAY DIFFRACTIONr_mcangle_it0.88325200
X-RAY DIFFRACTIONr_scbond_it1.46431854
X-RAY DIFFRACTIONr_scangle_it2.4354.51733
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 229 -
Rwork0.31 4344 -
obs--100 %

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