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- PDB-4kkx: Crystal structure of Tryptophan Synthase from Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 4kkx
TitleCrystal structure of Tryptophan Synthase from Salmonella typhimurium with 2-aminophenol quinonoid in the beta site and the F6 inhibitor in the alpha site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / carbon-oxygen lyase / tryptophan biosynthesis / F6F / allosteric enzyme / 2-aminophenol quinonoid / biosynthesis / aromatic amino acid biosynthesis / pyridoxal phosphate / LYASE-LYASE INHIBITOR complex
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-AQ3 / Chem-F6F / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsHilario, E. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: Biochemistry / Year: 2013
Title: Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.
Authors: Niks, D. / Hilario, E. / Dierkers, A. / Ngo, H. / Borchardt, D. / Neubauer, T.J. / Fan, L. / Mueller, L.J. / Dunn, M.F.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)73,57621
Polymers71,6182
Non-polymers1,95919
Water16,718928
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)147,15342
Polymers143,2354
Non-polymers3,91738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8550 Å2
ΔGint-34 kcal/mol
Surface area42610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.870, 61.460, 67.390
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-860-

HOH

21B-993-

HOH

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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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA / Cell line (production host): CB149 / Strain (production host): Escherichia coli / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Cell line (production host): CB149 / Strain (production host): Escherichia coli / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 947 molecules

#3: Chemical ChemComp-F6F / 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE, F6


Mass: 329.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11F3NO6P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-AQ3 / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-3-[(2-hydroxyphenyl)amino]-D-alanine


Mass: 427.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N3O8P
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 53.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-NaOH, 10-14% PEG 8000, 2 mM spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→91.626 Å / Num. all: 63604 / Num. obs: 63604 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.071 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.77-1.872.90.4641.62563388250.46482.9
1.87-1.982.90.3262.32331980660.32679.9
1.98-2.122.90.2143.52099873280.21477.4
2.12-2.292.80.1474.81910768570.14777.8
2.29-2.52.60.1076.61786368680.10784.5
2.5-2.82.50.0788.91752169880.07895
2.8-3.232.70.06111.91756364880.06199.4
3.23-3.962.90.04117.91615655010.041100
3.96-5.63.10.02725.31331043040.027100
5.6-29.4293.10.02426.1732823790.02499

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.3.20data scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPJ

4hpj


Resolution: 1.77→29.429 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8796 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 3237 5.09 %Random
Rwork0.1511 ---
obs0.1534 63561 86.83 %-
all-63561 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 18.7278 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: LAST / Resolution: 1.77→29.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 127 928 6064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115435
X-RAY DIFFRACTIONf_angle_d1.2997367
X-RAY DIFFRACTIONf_chiral_restr0.084804
X-RAY DIFFRACTIONf_plane_restr0.006976
X-RAY DIFFRACTIONf_dihedral_angle_d14.3792071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.79640.27061180.24192527264584
1.7964-1.82450.28881430.23222487263083
1.8245-1.85440.26011390.21112477261683
1.8544-1.88640.27091380.20082430256882
1.8864-1.92070.20421180.19552418253680
1.9207-1.95760.21271150.18712389250480
1.9576-1.99750.24471350.19092372250778
1.9975-2.0410.22661300.16612328245877
2.041-2.08840.21291170.15762308242578
2.0884-2.14060.21091020.15452340244277
2.1406-2.19850.20711370.14972320245777
2.1985-2.26320.191500.14822329247978
2.2632-2.33620.19891190.14872413253280
2.3362-2.41970.21371240.15052576270084
2.4197-2.51650.20871230.15592651277488
2.5165-2.63090.21231700.15742781295193
2.6309-2.76960.20241580.15522947310597
2.7696-2.94290.23691560.15422994315099
2.9429-3.16990.19981610.14629973158100
3.1699-3.48850.17511580.130530433201100
3.4885-3.99220.15131680.12530393207100
3.9922-5.02560.15531720.12130553227100
5.0256-29.43340.18851860.15683103328999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0006-0.00130.00030.00180.00030.00010.00040.00340.0029-0.0002-0.0038-0.005-0.0022-0.0052-00.04720.0070.00360.072-0.01120.0877-54.2542-18.213221.6897
20.0072-0.0072-0.00030.0061-0.00280.00080.0232-0.00640.0083-0.0174-0.03120.0219-0.0125-0.017300.00360.04270.0154-0.0014-0.02650.0596-42.9215-23.735921.3732
30.0004-0.00130.00090.0012-0.000600.00860.00530.0064-0.008-0.0038-0.0015-0.0116-0.0012-00.10110.0571-0.02350.0648-0.00940.111-48.497-9.607511.6687
40.00070.0006-0.00070.0004-0.00010.0002-0.0031-0.0026-0.00720.00090.00180.00050.0051-0.007700.0229-0.0055-0.00330.0236-0.01920.0246-30.5782-43.970612.9686
50.0008-0.0011-0.0026-0.00030.00310.0013-0.0185-0.0017-0.0089-0.0001-0.01920.00140.01320.005900.0207-0.00260.00480.0382-0.01250.019-4.8454-48.47774.8653
60.0058-0.0032-0.0074-0.00660.00780.016-0.0068-0.00480.0156-0.008-0.0218-0.0122-0.0170.0068-00.00720.00080.0360.0109-0.035-0.1466-11.8319-35.399913.6358
70.0004-0.00020.0002-0.0011-0.00080.001-0.009-0.00290.0001-0.00440.0021-0.0029-0.01610.0081-00.0274-0.01980.00240.03150.0113-0.00374.1663-31.86615.4966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 268 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 37 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 70 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 364 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 365 through 396 )B0

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