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- PDB-5bw6: Tryptophan Synthase from Salmonella typhimurium in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5bw6
TitleTryptophan Synthase from Salmonella typhimurium in complex with a single molecule of 2-({[4-(trifluoromethoxy)phenyl]carbonyl}amino)ethyl dihydrogen phosphate (F6) in the alpha-site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella typhimurium / F6F / inhibitor / allosteric enzyme / aromatic amino acid biosynthesis / pyridoxal phosphate / TRANSFERASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / 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-F6F / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHilario, E. / Caulkins, B.G. / Young, R.P. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097569 United States
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water.
Authors: Hilario, E. / Caulkins, B.G. / Huang, Y.M. / You, W. / Chang, C.E. / Mueller, L.J. / Dunn, M.F. / Fan, L.
History
DepositionJun 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)72,2175
Polymers71,6182
Non-polymers5993
Water11,710650
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)144,43410
Polymers143,2354
Non-polymers1,1996
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8430 Å2
ΔGint-27 kcal/mol
Surface area44310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.030, 58.900, 67.230
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-855-

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 / Plasmid: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / 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 / Plasmid: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 653 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 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


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50mM Bicine-NaOH, pH 7.8, containing 50mM NaCl, 2mM spermine, and 10% PEG 8000
PH range: 7.6 - 8.0 / Temp details: constant

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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 1, 2013 / Details: VariMax
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→20 Å / Num. all: 46573 / Num. obs: 46573 / % possible obs: 72.8 % / Redundancy: 2.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.035 / Rrim(I) all: 0.056 / Rsym value: 0.043 / Net I/σ(I): 13.1 / Num. measured all: 100061
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
1.82-1.922.10.45421382464450.7560.0140.01869.7
5.76-202.40.01834471919280.9990.0150.0291.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLM7.1.3data reduction
SCALA3.3.22data scaling
MOLREP11.3.02phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WX2

4wx2


Resolution: 1.82→19.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1933 / WRfactor Rwork: 0.15 / FOM work R set: 0.8322 / SU B: 6.18 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1798 / SU Rfree: 0.1588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2237 4.8 %RANDOM
Rwork0.1682 ---
obs0.1705 44334 72.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 25.879 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.05 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.82→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 37 673 5634
Biso mean--26.06 34.64 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195192
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9757036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41724.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6571533
X-RAY DIFFRACTIONr_chiral_restr0.1080.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213980
X-RAY DIFFRACTIONr_mcbond_it0.7051.1542662
X-RAY DIFFRACTIONr_mcangle_it1.2381.723345
X-RAY DIFFRACTIONr_scbond_it0.8751.2932528
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 149 -
Rwork0.339 3065 -
all-3214 -
obs--68.68 %
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)
11.1187-0.0529-0.01660.71710.09380.6930.16190.07990.0252-0.0676-0.09070.0209-0.1599-0.128-0.07120.09040.06170.02370.10140.01270.1633-48.6954-14.256421.1033
20.8564-0.2715-0.24350.7643-0.05180.16620.10480.00320.03550.022-0.0623-0.0089-0.0245-0.0338-0.04250.1050.02220.02170.1231-0.01040.1375-40.3079-21.780425.839
32.87351.4764-0.65912.58821.80242.7342-0.03210.3432-0.01630.0887-0.05910.16830.1388-0.26310.09120.01340.0147-0.02060.212-0.0750.1576-48.8165-33.33616.4887
40.66710.17440.34096.9948-2.89451.50580.00440.2043-0.0529-0.29820.18050.42680.1003-0.0678-0.18490.05410.0483-0.07430.3529-0.05190.1088-54.5717-30.193511.6343
55.05594.40841.40124.24120.81661.0797-0.05260.1464-0.1744-0.18980.1859-0.1339-0.1235-0.2272-0.13330.27510.16260.02320.19240.08210.1051-48.9673-12.78479.3388
67.73898.53262.32110.60322.79841.38230.16990.2950.4578-0.17690.01530.4483-0.1824-0.1305-0.18520.19050.14970.06390.13210.09730.2301-52.6362-5.030412.6498
71.10170.0816-0.99280.0235-0.0870.9167-0.07870.1474-0.09040.02150.02480.02140.0588-0.18920.05380.0981-0.0084-0.01470.2032-0.00310.1505-30.5793-42.134913.8981
80.54950.03030.1590.01530.07170.5753-0.00570.0785-0.0145-0.0131-0.0162-0.0050.01940.02730.02190.11850.0069-0.01370.1384-0.01130.1156-6.2925-43.96245.7231
90.8730.9248-0.25741.56480.39730.99930.17850.02820.06890.0028-0.0425-0.0517-0.134-0.1169-0.1360.17320.03970.02780.1367-0.0070.1266-16.9729-27.45170.0245
100.3664-0.2048-0.04450.1562-0.09320.4010.02750.00420.0008-0.0115-0.01130.00120.0256-0.0585-0.01620.1038-0.0026-0.02240.145-0.00180.1317-16.2613-37.669810.9851
110.66090.1282-0.14670.26470.14610.16040.0267-0.03730.10180.0124-0.00520.025-0.0090.0049-0.02140.11420.00870.00110.1308-0.01180.1352-14.7386-29.05224.4637
120.80530.0712-0.27190.01240.03640.7312-0.0023-0.01520.0045-0.00520.0095-0.0001-0.0520.036-0.00720.1029-0.001-0.01120.1328-0.00280.1333-2.5405-33.437120.4377
130.0734-0.19060.30350.9432-0.45912.22650.05260.0428-0.0216-0.11730.06260.1202-0.18090.4649-0.11520.1445-0.06080.03530.2028-0.0140.07074.4504-29.867915.6494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 61
2X-RAY DIFFRACTION2A62 - 159
3X-RAY DIFFRACTION3A160 - 179
4X-RAY DIFFRACTION4A193 - 216
5X-RAY DIFFRACTION5A217 - 247
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 100
9X-RAY DIFFRACTION9B101 - 151
10X-RAY DIFFRACTION10B152 - 244
11X-RAY DIFFRACTION11B245 - 301
12X-RAY DIFFRACTION12B302 - 364
13X-RAY DIFFRACTION13B365 - 396

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