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- PDB-6vnt: Tryptophan synthase in complex with inhibitor N-(4'-trifluorometh... -

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Basic information

Entry
Database: PDB / ID: 6vnt
TitleTryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the metal coordination site at 1.25 Angstrom resolution
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / protein complex / LYASE / Salmonella / 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. / Pyridoxal-phosphate dependent enzyme / 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. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-0JO / Chem-F9F / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsHilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: Tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the ...Title: Tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the metal coordination site at 1.25 Angstrom resolution.
Authors: Hilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)72,84512
Polymers71,6182
Non-polymers1,22710
Water16,214900
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)145,68924
Polymers143,2354
Non-polymers2,45420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12660 Å2
ΔGint-36 kcal/mol
Surface area42830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.022, 59.382, 67.322
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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Details (production host): 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 910 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.99 % / Description: Large plate-like crystal (200x100x50)
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
PH range: 7.8-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.000014 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2018 / Details: M2
RadiationMonochromator: Theta2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000014 Å / Relative weight: 1
ReflectionResolution: 1.25→91.174 Å / Num. obs: 187530 / % possible obs: 94.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.099 / Rsym value: 0.093 / Net I/av σ(I): 5 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.251-1.323.30.7071250290.4420.8360.70787
1.32-1.43.20.4841.5237220.3050.5730.48487.3
1.4-1.498.50.4431.6244710.1570.4710.44395.6
1.49-1.618.40.2862.4231000.1020.3050.28697
1.61-1.778.50.1943.5215280.0690.2060.19498.2
1.77-1.988.70.1314.9196430.0460.1390.13198.8
1.98-2.288.60.16.3173690.0360.1070.199.2
2.28-2.88.50.0887148100.0310.0930.08899.5
2.8-3.9510.60.0738.3115330.0240.0770.07399.8
3.95-36.2858.80.04314.663250.0160.0470.04398

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.45 Å36.29 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 187358
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.78-10035.80.9021198
4.79-6.7831.50.912350
3.92-4.79230.9442979
3.39-3.92220.9373529
3.03-3.3923.70.9323983
2.77-3.0324.60.9164405
2.56-2.7725.70.9144731
2.4-2.5624.50.9235077
2.26-2.423.20.9265430
2.14-2.2622.50.9345707
2.04-2.1422.90.9265929
1.96-2.0423.50.9276288
1.88-1.96240.9116483
1.81-1.8824.70.9096729
1.75-1.8125.40.9146947
1.7-1.7526.10.9147160
1.64-1.726.40.9157418
1.6-1.6426.80.9047627
1.56-1.6280.9077759
1.52-1.5629.10.97915
1.48-1.5229.50.9118118
1.45-1.4830.30.9018252
1.41-1.45330.8928411
1.38-1.4132.60.8978173
1.36-1.3835.20.8918007
1.33-1.3636.50.8848199
1.31-1.33390.8838258
1.28-1.3141.30.8728419
1.25-1.2846.20.82811877

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HN4

4hn4


Resolution: 1.25→36.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.667 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 9485 5.1 %RANDOM
Rwork0.1526 ---
obs0.154 177873 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.89 Å2 / Biso mean: 20.71 Å2 / Biso min: 6.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20.99 Å2
2--2.06 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.25→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 78 933 6020
Biso mean--26.27 37.53 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125620
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.6367652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01421.886281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55115960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1371540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024409
X-RAY DIFFRACTIONr_rigid_bond_restr1.03135620
LS refinement shellResolution: 1.25→1.284 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.265 652 -
Rwork0.247 11989 -
obs--86.55 %

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