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- PDB-6dzo: Crystal structure of Salmonella typhimurium Tryptophan Synthase m... -

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Entry
Database: PDB / ID: 6dzo
TitleCrystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE Inhibitor / Q114A / 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-F9F / Chem-KOU / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
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: Crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ...Title: Crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJul 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.3Oct 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)73,37929
Polymers71,1872
Non-polymers2,19127
Water12,322684
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)146,75758
Polymers142,3744
Non-polymers4,38354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18060 Å2
ΔGint-324 kcal/mol
Surface area42530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.349, 58.380, 67.300
Angle α, β, γ (deg.)90.000, 94.890, 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 beta-Q114A / Details (production host): mutation beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42488.367 Da / Num. of mol.: 1 / Mutation: Q114A
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 beta-Q114A / Details (production host): muattion beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 7 types, 711 molecules

#3: 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
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.49 Å3/Da / Density % sol: 50.66 % / Description: Large plate-like crystal
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50mM Bicine-CsOH pH 7.8, 50mM Cesium chloride, 9% PEG 8,000, 2mM spermine
PH range: 7.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cobra
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 80656 / % possible obs: 94.1 % / Observed criterion σ(F): 1.64 / Redundancy: 3.6 % / Biso Wilson estimate: 15.891 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.027 / Rrim(I) all: 0.048 / Net I/σ(I): 16.1
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 11260 / CC1/2: 0.985 / Rpim(I) all: 0.11 / Rrim(I) all: 0.172 / % possible all: 90.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.376
Highest resolutionLowest resolution
Rotation29.19 Å1.84 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 80593
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.89-10033.50.907566
6.29-8.8938.30.9151016
5.13-6.2936.10.8861306
4.44-5.1325.60.9241508
3.98-4.4424.60.931701
3.63-3.9824.50.9291895
3.36-3.6322.40.9352024
3.14-3.3623.30.9162193
2.96-3.1423.90.9252265
2.81-2.9623.90.9152414
2.68-2.8122.50.932538
2.57-2.6821.80.9322627
2.47-2.5721.40.9262770
2.38-2.4720.50.9282810
2.3-2.3819.70.932917
2.22-2.319.60.9293029
2.16-2.2218.80.9383063
2.1-2.1619.20.9273197
2.04-2.1190.9283202
1.99-2.0420.40.9243350
1.94-1.9919.20.9163369
1.9-1.9419.80.9233481
1.85-1.9200.923529
1.81-1.8520.50.9223571
1.78-1.8120.50.923638
1.74-1.7821.80.9153704
1.71-1.7423.10.913764
1.68-1.7124.20.9063784
1.64-1.6832.60.8685362

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
DM7.0.059phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPX

4hpx


Resolution: 1.64→29.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.885 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0987 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.093 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 3982 4.9 %RANDOM
Rwork0.1722 ---
obs0.1734 76612 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.15 Å2 / Biso mean: 21.996 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.21 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.64→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 101 713 5800
Biso mean--31.68 34.28 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125348
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.6487265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6322.328262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84515870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4331534
X-RAY DIFFRACTIONr_chiral_restr0.0930.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024076
LS refinement shellResolution: 1.64→1.682 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 273 -
Rwork0.242 5421 -
all-5694 -
obs--89.7 %
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)
10.4638-0.2610.00640.53370.02340.20310.0442-0.00820.04260.0249-0.041-0.0361-0.0086-0.0149-0.00320.03570.00770.00440.0148-0.00250.0612-40.53969.821724.7069
21.28770.0263-0.25240.7189-0.16430.38810.15260.2465-0.1270.0198-0.12860.0390.0061-0.0931-0.0240.03630.0191-0.0410.0905-0.02690.058-46.6345-1.294714.0774
33.65594.8849-3.85646.8876-6.17188.037-0.22690.378-0.3146-0.40030.3632-0.2070.2997-0.3744-0.13620.08890.0915-0.06990.2148-0.16080.171-54.3848-2.49497.341
40.53440.11980.04890.6338-0.08910.20450.08790.10610.028-0.0348-0.06180.0078-0.0139-0.0421-0.02610.03960.0329-0.01060.05780.02140.039-49.563812.015310.5475
54.90123.69271.24584.0050.93060.62950.01480.04340.3517-0.2104-0.09050.1393-0.1276-0.15190.07570.10620.08840.01150.09980.03020.074-52.122124.005612.5125
61.1162-0.0832-0.84950.00930.05440.6792-0.06990.124-0.14580.0086-0.00510.02190.0399-0.13460.0750.0360.0121-0.00870.07760.00220.0913-30.4126-13.111514.0855
70.66190.27750.25850.27450.3050.4338-0.03090.0919-0.03140.01580.01430.02170.060.08250.01660.03850.0135-0.01540.0842-0.01090.0293-4.0094-17.62195.7411
80.4194-0.12550.2530.1160.09020.5070.02690.0282-0.0433-0.0224-0.01350.0168-0.02160.0187-0.01330.0485-0.0053-0.02550.0527-0.00190.0344-8.7717-11.99715.8511
90.13010.2962-0.13321.76650.36490.58110.07170.027-0.0048-0.0548-0.0105-0.0843-0.1814-0.0556-0.06120.10250.02390.00060.0438-0.01040.0197-17.55072.90360.7976
100.2719-0.1331-0.11840.1079-0.0510.34070.00320.0362-0.03190.0052-0.01480.0101-0.0006-0.03380.01170.04260.0023-0.02550.0493-0.00520.0447-15.4437-11.383512.3697
110.49380.1106-0.03240.07330.03110.0389-0.0089-0.0710.097-0.0075-0.00810.03380.00210.00370.0170.0370.0025-0.01530.0472-0.0230.0644-14.5943-0.020324.6142
120.56950.2262-0.05510.10830.06180.4877-0.0053-0.04440.0263-0.0127-0.00450.0128-0.0370.00570.00970.03940.0013-0.01450.0422-0.00480.0438-5.2754-4.331421.0617
130.1606-0.22040.050.3035-0.09660.78510.0301-0.02990.0095-0.03730.0395-0.0101-0.09910.0661-0.06960.0502-0.0132-0.00350.0642-0.00680.03063.669-3.074717.0807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 187
3X-RAY DIFFRACTION3A188 - 202
4X-RAY DIFFRACTION4A203 - 247
5X-RAY DIFFRACTION5A248 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 70
8X-RAY DIFFRACTION8B71 - 100
9X-RAY DIFFRACTION9B101 - 165
10X-RAY DIFFRACTION10B166 - 244
11X-RAY DIFFRACTION11B245 - 301
12X-RAY DIFFRACTION12B302 - 343
13X-RAY DIFFRACTION13B344 - 395

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