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- PDB-6l8a: Tetrathionate hydrolase from Acidithiobacillus ferrooxidans -

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Basic information

Entry
Database: PDB / ID: 6l8a
TitleTetrathionate hydrolase from Acidithiobacillus ferrooxidans
ComponentsTetrathionate hydrolase
KeywordsHYDROLASE / Tetrathionate
Function / homology
Function and homology information


Hydrolases; Acting on sulfur-sulfur bonds / hydrolase activity / plasma membrane
Similarity search - Function
PQQ-like domain / PQQ enzyme repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
BETA-ALANINE / GLYCINE / Tetrathionate hydrolase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95004814203 Å
AuthorsTamada, T. / Hirano, Y.
CitationJournal: Protein Sci. / Year: 2020
Title: Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans.
Authors: Kanao, T. / Hase, N. / Nakayama, H. / Yoshida, K. / Nishiura, K. / Kosaka, M. / Kamimura, K. / Hirano, Y. / Tamada, T.
History
DepositionNov 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Tetrathionate hydrolase
B: Tetrathionate hydrolase
C: Tetrathionate hydrolase
D: Tetrathionate hydrolase
E: Tetrathionate hydrolase
F: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,58341
Polymers300,2836
Non-polymers3,29935
Water12,556697
1
A: Tetrathionate hydrolase
C: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,14413
Polymers100,0942
Non-polymers1,05011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-136 kcal/mol
Surface area27710 Å2
MethodPISA
2
B: Tetrathionate hydrolase
D: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,62418
Polymers100,0942
Non-polymers1,53016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-201 kcal/mol
Surface area27610 Å2
MethodPISA
3
E: Tetrathionate hydrolase
F: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,81410
Polymers100,0942
Non-polymers7208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-136 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.026, 91.026, 231.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32

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Components

#1: Protein
Tetrathionate hydrolase / TTH


Mass: 50047.230 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: B7J3C9, Hydrolases; Acting on sulfur-sulfur bonds
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BAL / BETA-ALANINE / Β-Alanine


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H7NO2
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: sodium chloride, glycine, PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→42.4 Å / Num. obs: 156219 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.7759592713 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.109 / Net I/av σ(I): 10.3 / Net I/σ(I): 20.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 15660 / CC1/2: 0.875 / Rrim(I) all: 0.563 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95004814203→42.3647721231 Å / SU ML: 0.227474103365 / Cross valid method: FREE R-VALUE / σ(F): 1.96795806727 / Phase error: 23.0146924341
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219118522569 8100 5.18801760083 %
Rwork0.176950396019 148029 -
obs0.179181906088 156129 99.6947773727 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7975605035 Å2
Refinement stepCycle: LAST / Resolution: 1.95004814203→42.3647721231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20427 0 178 697 21302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007179673771721198
X-RAY DIFFRACTIONf_angle_d0.96271930995929031
X-RAY DIFFRACTIONf_chiral_restr0.06221836520783133
X-RAY DIFFRACTIONf_plane_restr0.008149303313173725
X-RAY DIFFRACTIONf_dihedral_angle_d10.876615724611999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95004814203-1.97220.2953100371612680.2314011994594967X-RAY DIFFRACTION99.9236495514
1.9722-1.99540.3080257667022720.2304581126394910X-RAY DIFFRACTION99.9228692634
1.9954-2.01970.2739164169283300.2180296010874914X-RAY DIFFRACTION100
2.0197-2.04530.2724450242132340.2107400052494936X-RAY DIFFRACTION99.8840803709
2.0453-2.07220.2920999069062480.2135215886695028X-RAY DIFFRACTION99.8674995268
2.0722-2.10060.2727856397772560.2109135115444886X-RAY DIFFRACTION99.8834498834
2.1006-2.13060.2752202737122300.2103903645735072X-RAY DIFFRACTION99.8681484272
2.1306-2.16240.2558766727232560.1990703389854901X-RAY DIFFRACTION99.9224956404
2.1624-2.19620.2395520476093100.1918259304644864X-RAY DIFFRACTION99.8841698842
2.1962-2.23220.2564404967892600.1905888014634997X-RAY DIFFRACTION99.8480531814
2.2322-2.27070.2400933573262960.1866139921924923X-RAY DIFFRACTION99.8087588449
2.2707-2.3120.2481624644572500.1930635657834930X-RAY DIFFRACTION99.8843038951
2.312-2.35650.2563351861172300.1930364353645020X-RAY DIFFRACTION99.8098859316
2.3565-2.40450.2419151000882770.1946152616744931X-RAY DIFFRACTION99.8466257669
2.4045-2.45680.2770011258542580.1948848974884972X-RAY DIFFRACTION99.9044890162
2.4568-2.5140.2666750311512930.1987426318834893X-RAY DIFFRACTION99.8075442648
2.514-2.57680.2506187876882680.1937077159874933X-RAY DIFFRACTION99.7315436242
2.5768-2.64650.2581480596312710.2001231759594945X-RAY DIFFRACTION99.7132479449
2.6465-2.72440.2630987818042340.2005668143994938X-RAY DIFFRACTION99.7877677021
2.7244-2.81230.2551432500552330.2006903816364997X-RAY DIFFRACTION99.7520503529
2.8123-2.91280.2429262328223170.2008944795654912X-RAY DIFFRACTION99.6569468268
2.9128-3.02940.2544759971292640.1972100037944919X-RAY DIFFRACTION99.4817658349
3.0294-3.16720.2187790129112470.1937128515934948X-RAY DIFFRACTION99.4829567216
3.1672-3.33410.2347619054062420.1867488929594934X-RAY DIFFRACTION99.3664810904
3.3341-3.54290.2055021792042920.1650822575584860X-RAY DIFFRACTION99.0388312188
3.5429-3.81630.1830313359693440.1505814658954876X-RAY DIFFRACTION99.1641337386
3.8163-4.20.1656091013312680.1367872108264868X-RAY DIFFRACTION99.1697238849
4.2-4.8070.1611509871052870.1314765237514933X-RAY DIFFRACTION99.2584141472
4.807-6.05360.168077216392860.1458834943964929X-RAY DIFFRACTION99.6560290464
6.0536-100.1837706778952790.1657252202654893X-RAY DIFFRACTION99.5572666025

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