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- PDB-7cqy: Tetrathionate hydrolase from Acidithiobacillus ferrooxidans mutan... -

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Basic information

Entry
Database: PDB / ID: 7cqy
TitleTetrathionate hydrolase from Acidithiobacillus ferrooxidans mutant - D325N
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
Tetrathionate hydrolase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8003577513 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
DepositionAug 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)301,14215
Polymers300,2776
Non-polymers8659
Water18010
1
A: Tetrathionate hydrolase
C: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1893
Polymers100,0922
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-30 kcal/mol
Surface area28310 Å2
MethodPISA
2
B: Tetrathionate hydrolase
D: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3815
Polymers100,0922
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-96 kcal/mol
Surface area27940 Å2
MethodPISA
3
E: Tetrathionate hydrolase
F: Tetrathionate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5737
Polymers100,0922
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-104 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.315, 94.315, 235.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA34 - 1125 - 83
12GLYGLYSERSER(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA116 - 18887 - 159
13SERSERTHRTHR(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA213 - 314184 - 285
14ASNASNASPASP(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA325 - 338296 - 309
15SERSERASNASN(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA352 - 370323 - 341
16GLYGLYTHRTHR(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA382 - 420353 - 391
17ALAALAILEILE(chain A and (resseq 34:112 or resseq 116:188 or resseq...AA426 - 495397 - 466
28VALVALSERSER(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB34 - 1125 - 83
29GLYGLYSERSER(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB116 - 18887 - 159
210SERSERTHRTHR(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB213 - 314184 - 285
211ASNASNASPASP(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB325 - 338296 - 309
212SERSERASNASN(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB352 - 370323 - 341
213GLYGLYTHRTHR(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB382 - 420353 - 391
214ALAALAILEILE(chain B and (resseq 34:112 or resseq 116:188 or resseq...BB426 - 495397 - 466
315VALVALSERSER(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC34 - 1125 - 83
316GLYGLYSERSER(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC116 - 18887 - 159
317SERSERTHRTHR(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC213 - 314184 - 285
318ASNASNASPASP(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC325 - 338296 - 309
319SERSERASNASN(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC352 - 370323 - 341
320GLYGLYTHRTHR(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC382 - 420353 - 391
321ALAALAILEILE(chain C and (resseq 34:112 or resseq 116:188 or resseq...CC426 - 495397 - 466
422VALVALSERSER(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD34 - 1125 - 83
423GLYGLYSERSER(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD116 - 18887 - 159
424SERSERTHRTHR(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD213 - 314184 - 285
425ASNASNASPASP(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD325 - 338296 - 309
426SERSERASNASN(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD352 - 370323 - 341
427GLYGLYTHRTHR(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD382 - 420353 - 391
428ALAALAILEILE(chain D and (resseq 34:112 or resseq 116:188 or resseq...DD426 - 495397 - 466
529VALVALSERSER(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE34 - 1125 - 83
530GLYGLYSERSER(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE116 - 18887 - 159
531SERSERTHRTHR(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE213 - 314184 - 285
532ASNASNASPASP(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE325 - 338296 - 309
533SERSERASNASN(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE352 - 370323 - 341
534GLYGLYTHRTHR(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE382 - 420353 - 391
535ALAALAILEILE(chain E and (resseq 34:112 or resseq 116:188 or resseq...EE426 - 495397 - 466
636VALVALSERSER(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF34 - 1125 - 83
637GLYGLYSERSER(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF116 - 18887 - 159
638SERSERTHRTHR(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF213 - 314184 - 285
639ASNASNASPASP(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF325 - 338296 - 309
640SERSERASNASN(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF352 - 370323 - 341
641GLYGLYTHRTHR(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF382 - 420353 - 391
642ALAALAILEILE(chain F and (resseq 34:112 or resseq 116:188 or resseq...FF426 - 495397 - 466

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Components

#1: Protein
Tetrathionate hydrolase / TTH


Mass: 50046.246 Da / Num. of mol.: 6 / Mutation: D325N
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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG1000, sodium chloride, glycine

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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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.2400980047 Å / Num. obs: 57563 / % possible obs: 99.53 % / Redundancy: 5.1 % / Biso Wilson estimate: 61.5415232325 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07656 / Rpim(I) all: 0.03766 / Rrim(I) all: 0.08548 / Net I/σ(I): 16.49
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5572 / Mean I/σ(I) obs: 2.74 / Num. unique obs: 5788 / CC1/2: 0.776 / CC star: 0.935 / Rpim(I) all: 0.2941 / Rrim(I) all: 0.6319 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L8A

6l8a


Resolution: 2.8003577513→46.2400980047 Å / SU ML: 0.474375557846 / Cross valid method: FREE R-VALUE / σ(F): 1.96792060498 / Phase error: 32.9454907305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.280094520069 2770 4.8201576557 %
Rwork0.225293551501 54697 -
obs0.227938799273 57467 99.5513286907 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.0428490964 Å2
Refinement stepCycle: LAST / Resolution: 2.8003577513→46.2400980047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19882 0 45 10 19937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031761823684120524
X-RAY DIFFRACTIONf_angle_d0.73621045834628112
X-RAY DIFFRACTIONf_chiral_restr0.05285927984423058
X-RAY DIFFRACTIONf_plane_restr0.005662170572563615
X-RAY DIFFRACTIONf_dihedral_angle_d8.0645147326811658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.84860.4269188444421560.3327351505742759X-RAY DIFFRACTION99.6922024624
2.8486-2.90040.4816819638941370.3420978203322730X-RAY DIFFRACTION99.7564370216
2.9004-2.95620.3458689934761290.3270521467172784X-RAY DIFFRACTION99.7261211914
2.9562-3.01650.3763876924071760.2864639014662696X-RAY DIFFRACTION99.7222222222
3.0165-3.08210.4428121593251480.2806595485972703X-RAY DIFFRACTION99.5460893855
3.0821-3.15380.315416739251030.2819546063982796X-RAY DIFFRACTION99.6562392575
3.1538-3.23260.2990913289171350.2579519314162705X-RAY DIFFRACTION99.5792426367
3.2326-3.320.3771465969151120.2625090451892726X-RAY DIFFRACTION99.3697478992
3.32-3.41770.3192134966211520.2630247602742749X-RAY DIFFRACTION99.656475438
3.4177-3.5280.3379978030651200.2662624384032736X-RAY DIFFRACTION99.7206703911
3.528-3.6540.3429377619661410.244853141832744X-RAY DIFFRACTION99.5170748534
3.654-3.80020.3217140462261390.2347290620922747X-RAY DIFFRACTION99.7235659986
3.8002-3.97310.2556803439821530.219241848652727X-RAY DIFFRACTION99.6884735202
3.9731-4.18250.2696774387791380.211818862462722X-RAY DIFFRACTION99.3055555556
4.1825-4.44430.2421881590311300.1998177533052748X-RAY DIFFRACTION99.550328606
4.4443-4.78710.2488251595691590.188465933272712X-RAY DIFFRACTION99.445791479
4.7871-5.26830.191026155891130.176063843362739X-RAY DIFFRACTION98.9247311828
5.2683-6.02920.2352837388891680.2005847938512689X-RAY DIFFRACTION99.3393602225
6.0292-7.59070.2447922858121260.2119820013782734X-RAY DIFFRACTION99.6863018473
7.5907-46.24009800470.2250039524051350.1923061450122751X-RAY DIFFRACTION99.4143988977

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