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- PDB-4y6g: Crystal structure of Tryptophan Synthase from Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 4y6g
TitleCrystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and beta-site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / lyase / tryptophan biosynthesis / Salmonella typhimurium / F6F / inhibitor / allosteric enzyme / aromatic amino acid biosynthesis / pyridoxal phosphate / LYASE-LYASE INHIBITOR complex
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
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: 1.65 Å
AuthorsHilario, E. / Caulkins, B.G. / Young, R.P. / 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
DepositionFeb 13, 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)72,5466
Polymers71,6182
Non-polymers9284
Water13,187732
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)145,09212
Polymers143,2354
Non-polymers1,8578
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area8610 Å2
ΔGint-32 kcal/mol
Surface area44970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.170, 59.840, 67.300
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number5
Space group name H-MC121

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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, 736 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.: 2 / 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.: 732 / 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: 52.32 % / Description: Large plate-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, 10% PEG 8,000, 2 mM spermine, pH 7.8, 100mM NaCl
PH range: 7.4-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2013 / Details: Rigaku VariMax
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→91.747 Å / Num. all: 87302 / Num. obs: 87302 / % possible obs: 99.4 % / Redundancy: 3.2 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Rsym value: 0.046 / Net I/av σ(I): 9.396 / Net I/σ(I): 11.9 / Num. measured all: 276270
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.65-1.7430.4581.637626124710.310.4582.398
1.74-1.843.10.2862.636692119230.1930.2863.798.9
1.84-1.973.10.184.235386113010.120.185.899.5
1.97-2.133.20.1126.733466105590.0750.1128.999.8
2.13-2.333.20.0749.93115797540.050.07412.4100
2.33-2.613.20.05413.32866788580.0360.05415.5100
2.61-3.013.30.04315.82545178140.0280.04319.5100
3.01-3.693.30.03816.12178766350.0240.03825.2100
3.69-5.223.30.02217.21689551440.0140.02229100
5.22-21.6893.20.02118.3914328430.0140.02127.598.3

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Phasing

Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.94-10033.20.928549
6.32-8.9441.10.9071047
5.16-6.3234.20.9081329
4.47-5.1624.90.941583
4-4.4722.10.9461782
3.65-421.90.941978
3.38-3.65220.9372118
3.16-3.3822.20.9252282
2.98-3.1622.30.9322417
2.83-2.9821.60.9312556
2.7-2.8320.40.9332676
2.58-2.7190.9422830
2.48-2.5819.20.9332910
2.39-2.4818.50.9393061
2.31-2.3917.50.9473102
2.24-2.3117.40.9443297
2.17-2.2417.40.9433356
2.11-2.1717.10.9453443
2.05-2.1117.50.9413568
2-2.0518.20.943628
1.95-217.50.9413716
1.91-1.9518.90.9413799
1.86-1.9120.30.9323851
1.83-1.8621.40.9323989
1.79-1.8322.50.9263998
1.75-1.7923.50.9254096
1.72-1.7525.40.9184159
1.69-1.7226.40.9124233
1.65-1.6935.20.8565933

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.22data scaling
MOLREP11.2.08phasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WX2

4wx2


Resolution: 1.65→21.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1789 / WRfactor Rwork: 0.1544 / FOM work R set: 0.8705 / SU B: 3.454 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0836 / SU Rfree: 0.0801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1791 4376 5 %RANDOM
Rwork0.1582 ---
obs0.1592 82910 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.8 Å2 / Biso mean: 26.773 Å2 / Biso min: 2.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.65→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4943 0 58 761 5762
Biso mean--27.74 36.13 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195217
X-RAY DIFFRACTIONr_bond_other_d0.0010.024987
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9817069
X-RAY DIFFRACTIONr_angle_other_deg0.789311481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75424.089225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06415864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9991534
X-RAY DIFFRACTIONr_chiral_restr0.0880.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0216005
X-RAY DIFFRACTIONr_gen_planes_other0.020.021173
X-RAY DIFFRACTIONr_mcbond_it1.1382.332664
X-RAY DIFFRACTIONr_mcbond_other1.1382.3272663
X-RAY DIFFRACTIONr_mcangle_it1.7963.9133344
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 325 -
Rwork0.337 5967 -
all-6292 -
obs--97.44 %
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)
12.39930.98970.23992.18450.93280.736-0.03290.00560.1285-0.0906-0.12330.0901-0.2078-0.21040.15620.09240.0847-0.06930.087-0.0520.0692-49.041545.1859-11.0068
20.759-0.1670.12170.71970.15130.07010.0307-0.02110.0575-0.0428-0.05540.0101-0.0071-0.01130.02460.03090.01210.00180.0686-0.01170.0492-37.719637.2477-8.5938
31.9740.29570.40892.40771.02972.14290.13690.2371-0.1453-0.0568-0.12660.20460.0075-0.0002-0.01030.03250.0314-0.04060.0888-0.03830.0614-45.875225.2187-17.9396
46.62113.7857-2.87684.5851-4.55515.2549-0.17710.5861-0.2972-0.58240.46690.28150.2988-0.5622-0.28980.35370.0588-0.16890.1114-0.03950.1283-53.332624.5216-24.26
50.74330.06230.64221.02650.53170.8902-0.12850.08490.1093-0.3242-0.03020.0847-0.265-0.06630.15870.1391-0.0048-0.07170.1448-0.00810.068-48.117845.9251-21.7322
61.0135-0.1326-0.61510.03740.10470.41110.01070.1361-0.09710.023-0.06260.00110.0124-0.16320.05190.0424-0.0193-0.02440.2032-0.0120.0228-28.014316.2869-20.0426
70.42340.05680.04850.05330.13410.3838-0.03080.0309-0.0144-0.011-0.00320.0134-0.00520.02240.0340.05360.0029-0.0210.0892-0.00640.0231-3.460214.1708-27.715
81.53790.3041-1.10110.56-0.1090.8240.16250.01850.3076-0.03930.06460.0872-0.1113-0.0076-0.22720.06590.01170.00190.10570.00610.0823-17.825530.5627-30.908
90.3248-0.0426-0.04860.01680.05270.2795-0.0066-0.0393-0.0189-0.0032-0.0150.00880.0251-0.0250.02150.04860.0078-0.01560.08810.00130.0341-5.275715.4794-15.2456
103.38450.2159-0.14560.20730.20510.2440.07160.02320.35040.0691-0.03540.00610.0696-0.0384-0.03620.03430.0149-0.00310.07060.00040.0825-16.821531.8955-9.1636
110.58920.1441-0.19310.06640.01310.35080.002-0.03180.0623-0.00610.02540.0197-0.02620.0203-0.02740.04470.0005-0.01380.0912-0.00780.02580.44424.7185-13.2625
120.3089-0.211-0.16130.3119-0.21050.84860.09540.0028-0.0022-0.02540.00790.0401-0.13640.1177-0.10330.0634-0.02250.00990.1298-0.02590.01577.27428.6201-17.9887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2A43 - 159
3X-RAY DIFFRACTION3A160 - 180
4X-RAY DIFFRACTION4A181 - 202
5X-RAY DIFFRACTION5A203 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 100
8X-RAY DIFFRACTION8B101 - 196
9X-RAY DIFFRACTION9B197 - 269
10X-RAY DIFFRACTION10B270 - 301
11X-RAY DIFFRACTION11B302 - 364
12X-RAY DIFFRACTION12B365 - 397

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