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- PDB-8sy8: Crystal structure of TsaC -

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Basic information

Entry
Database: PDB / ID: 8sy8
TitleCrystal structure of TsaC
Components4-formylbenzenesulfonate dehydrogenase TsaC
KeywordsOXIDOREDUCTASE / Short chain dehydrogenase/reductase / Rossmann fold / NAD(H)binding
Function / homology4-formylbenzenesulfonate dehydrogenase / 4-formylbenzenesulfonate dehydrogenase activity / catabolic process / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 4-formylbenzenesulfonate dehydrogenase TsaC1/TsaC2
Function and homology information
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBoggs, D.G. / Tian, J. / Bridwell-Rabb, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138271 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The NADH recycling enzymes TsaC and TsaD regenerate reducing equivalents for Rieske oxygenase chemistry.
Authors: Tian, J. / Boggs, D.G. / Donnan, P.H. / Barroso, G.T. / Garcia, A.A. / Dowling, D.P. / Buss, J.A. / Bridwell-Rabb, J.
History
DepositionMay 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-formylbenzenesulfonate dehydrogenase TsaC
B: 4-formylbenzenesulfonate dehydrogenase TsaC


Theoretical massNumber of molelcules
Total (without water)57,4792
Polymers57,4792
Non-polymers00
Water1,51384
1
A: 4-formylbenzenesulfonate dehydrogenase TsaC
B: 4-formylbenzenesulfonate dehydrogenase TsaC

A: 4-formylbenzenesulfonate dehydrogenase TsaC
B: 4-formylbenzenesulfonate dehydrogenase TsaC


Theoretical massNumber of molelcules
Total (without water)114,9584
Polymers114,9584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area7440 Å2
ΔGint-60 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.700, 115.700, 66.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein 4-formylbenzenesulfonate dehydrogenase TsaC / TsaC / Toluenesulfonate zinc-independent alcohol dehydrogenase TsaC


Mass: 28739.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: tsaC1, tsaC, tsaC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P94681, 4-formylbenzenesulfonate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M KCl, 20% polyethylene glycol 3350, and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.18→43.59 Å / Num. obs: 26991 / % possible obs: 99.94 % / Redundancy: 16.68 % / Biso Wilson estimate: 54.61 Å2 / CC1/2: 1 / Rrim(I) all: 0.072 / Net I/σ(I): 24.18
Reflection shellResolution: 2.18→2.32 Å / Num. unique obs: 2670 / CC1/2: 0.72 / Rrim(I) all: 1.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDS20220110data reduction
XDS20220110data scaling
PHENIX1.20.1_4487phasing
Coot0.9.8.5model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→43.59 Å / SU ML: 0.2712 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 1350 5 %
Rwork0.2084 25633 -
obs0.2095 26983 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.28 Å2
Refinement stepCycle: LAST / Resolution: 2.18→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 0 84 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993210
X-RAY DIFFRACTIONf_angle_d1.36974370
X-RAY DIFFRACTIONf_chiral_restr0.0789507
X-RAY DIFFRACTIONf_plane_restr0.0219584
X-RAY DIFFRACTIONf_dihedral_angle_d12.1511124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.260.32761360.30512533X-RAY DIFFRACTION99.96
2.26-2.350.291330.26012541X-RAY DIFFRACTION100
2.35-2.450.331330.27322535X-RAY DIFFRACTION100
2.46-2.580.30731300.25692540X-RAY DIFFRACTION100
2.58-2.750.29631370.26112542X-RAY DIFFRACTION99.96
2.75-2.960.27021300.24282551X-RAY DIFFRACTION99.96
2.96-3.260.27551350.25332566X-RAY DIFFRACTION100
3.26-3.730.22781370.20482568X-RAY DIFFRACTION99.96
3.73-4.690.21631360.17762581X-RAY DIFFRACTION100
4.7-43.590.17341430.17922676X-RAY DIFFRACTION99.75

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