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- PDB-4zqc: Tryptophan Synthase from Salmonella typhimurium in complex with t... -

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Basic information

Entry
Database: PDB / ID: 4zqc
TitleTryptophan Synthase from Salmonella typhimurium in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and a single F6F molecule in the beta-site at 1.54 Angstrom resolution.
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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
DepositionMay 8, 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 / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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)73,81319
Polymers71,6182
Non-polymers2,19517
Water14,970831
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)147,62638
Polymers143,2354
Non-polymers4,39034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8630 Å2
ΔGint-22 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.529, 58.630, 67.220
Angle α, β, γ (deg.)90.000, 94.920, 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 , 5 types, 848 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.: 3 / Source method: obtained synthetically / Formula: C10H11F3NO6P
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 831 / 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: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, containing 10-14% PEG 8,000, and 2 mM spermine
PH range: 7.4 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2015
RadiationMonochromator: Kohzu Dual Double Crystal Monochromator (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. all: 99870 / Num. obs: 99870 / % possible obs: 95 % / Redundancy: 3.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.063 / Rrim(I) all: 0.123 / Rsym value: 0.105 / Net I/σ(I): 7.2 / Num. measured all: 376716
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
1.54-1.623.80.5562.153926141390.8130.0260.04492.4
4.87-304.10.04414.51378233870.990.0380.06298.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Blu-Ice4.5data collection
SCALA3.3.22data scaling
MOLREP11.3.02phasing
DM6.5.008phasing
PDB_EXTRACT3.15data extraction
iMOSFLM7.1.3data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6G

4y6g


Resolution: 1.54→29.31 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.141 / FOM work R set: 0.8432 / SU B: 3.479 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0862 / SU Rfree: 0.0761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 4955 5 %RANDOM
Rwork0.1357 ---
obs0.1382 94912 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 20.132 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0.05 Å2
2---0.33 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.54→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 127 869 6014
Biso mean--22.66 33.88 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195443
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.997378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56924.077233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06615898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9311537
X-RAY DIFFRACTIONr_chiral_restr0.1140.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214162
X-RAY DIFFRACTIONr_mcbond_it1.8631.4252759
X-RAY DIFFRACTIONr_mcangle_it2.4562.1473482
X-RAY DIFFRACTIONr_scbond_it2.6081.7072684
X-RAY DIFFRACTIONr_rigid_bond_restr2.37135443
X-RAY DIFFRACTIONr_sphericity_free39.1055255
X-RAY DIFFRACTIONr_sphericity_bonded19.1355945
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 356 -
Rwork0.212 6775 -
all-7131 -
obs--92.06 %
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)
10.10510.0219-0.00960.09650.02660.02360.00890.00210.00780.0025-0.00430.0053-0.0035-0.0003-0.00460.01260.0003-0.00730.03670.00070.0098-52.2312-13.117322.2374
20.03650.0067-0.01840.03830.00050.01590.00190.00120.00270.00080.0008-0.0041-0.00120.0008-0.00270.01190-0.00880.03520.00040.0077-40.4239-20.964624.8536
30.1644-0.08290.02240.06780.0610.22240.0070.0305-0.005-0.0005-0.01790.00340.00530.02040.01090.00820.0033-0.00770.04610.00320.0101-47.2419-32.099310.9337
40.0650.0646-0.07960.2605-0.09190.1112-0.01140.0088-0.0058-0.01330.008-0.00430.0126-0.00840.00350.0108-0.0011-0.00680.0377-0.00040.0093-54.8031-30.021110.8612
50.13910.10650.02910.18320.05210.02470.003-0.00080.0091-0.0108-0.0015-0.0046-0.0062-0.0011-0.00150.01310.0008-0.00640.03980.00060.0082-50.9071-8.980611.0727
60.07230.0016-0.00860.02010.00010.0194-0.0020.0066-0.00420.00310.00150.00390.0017-00.00050.0137-0-0.00980.0403-0.00030.0094-15.1762-43.16328.693
70.11730.0364-0.06820.0868-0.02220.06330.0186-0.00060.0219-0.0016-0.00120.0009-0.0129-0.0012-0.01740.01510.0007-0.00510.03850.00060.0137-20.9371-27.36822.5938
80.10180.0022-0.05520.02360.00610.04780.0067-0.00140.00840.0015-0.00120.0015-0.00160.001-0.00550.0131-0.0003-0.00940.03970.00030.0088-8.2083-35.64320.2508
90.0651-0.0472-0.0320.12340.00610.10840.0143-0.00160.0158-0.01550.0012-0.0106-0.01190.0056-0.01550.0128-0.0023-0.00420.0434-0.00060.0124.4829-29.280315.6452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2A43 - 159
3X-RAY DIFFRACTION3A160 - 190
4X-RAY DIFFRACTION4A191 - 216
5X-RAY DIFFRACTION5A217 - 268
6X-RAY DIFFRACTION6B2 - 100
7X-RAY DIFFRACTION7B101 - 196
8X-RAY DIFFRACTION8B197 - 364
9X-RAY DIFFRACTION9B365 - 397

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