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- PDB-8q9y: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -

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Basic information

Entry
Database: PDB / ID: 8q9y
TitleThe structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / copper enzyme / trinuclear copper center / atomic resolution / conformational changes / complex with inhibitor / thiourea / Pelomicrobium methylotrophicum
Function / homology
Function and homology information


Nitrous oxide reductase, N-terminal / : / Quinoprotein amine dehydrogenase, beta chain-like / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / THIOUREA / Twin-arginine translocation signal domain-containing protein
Similarity search - Component
Biological speciesPelomicrobium methylotrophicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVarfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-30004 Russian Federation
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Molecular mechanism of thiocyanate dehydrogenase at atomic resolution.
Authors: Varfolomeeva, L.A. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Khrenova, M.G. / Tikhonova, T.V. / Popov, V.O.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Twin-arginine translocation signal domain-containing protein
B: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,01914
Polymers108,1872
Non-polymers83212
Water23,1491285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-143 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.710, 96.670, 147.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Twin-arginine translocation signal domain-containing protein


Mass: 54093.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelomicrobium methylotrophicum (bacteria)
Gene: FR698_09980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C7ETD9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TOU / THIOUREA


Mass: 76.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 357145 / % possible obs: 93 % / Redundancy: 2.8 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.03 / Net I/σ(I): 17.52
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.150.321453830.8540.3951
1.15-1.20.237378680.9180.2871
1.2-1.30.175595110.9550.2111
1.3-1.40.117441620.980.141
1.4-1.50.08328840.990.0961
1.5-1.70.05435660.9960.0611
1.7-1.90.032267040.9980.0391
1.9-2.020.025115020.9990.031
2.02-2.150.02296600.9990.0271
2.15-2.320.02194390.9990.0251
2.32-2.540.01987960.9990.0231
2.54-2.840.01779460.9990.0211
2.84-3.280.01569180.9990.0181
3.28-40.014564810.0171
4-100.012671610.0141
10-500.0134420.9990.0161

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→39.17 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.756 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1246 15786 4.4 %RANDOM
Rwork0.10729 ---
obs0.10814 341358 92.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--1.4 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.1→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7283 0 25 1285 8593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0127730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157065
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.64310493
X-RAY DIFFRACTIONr_angle_other_deg0.7261.56316374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2245951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08622.403362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.141151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2191538
X-RAY DIFFRACTIONr_chiral_restr0.1370.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4273771
X-RAY DIFFRACTIONr_mcbond_other1.4273770
X-RAY DIFFRACTIONr_mcangle_it1.8362.9364714
X-RAY DIFFRACTIONr_mcangle_other1.8365.0994715
X-RAY DIFFRACTIONr_scbond_it2.3963958
X-RAY DIFFRACTIONr_scbond_other2.3953953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6575771
X-RAY DIFFRACTIONr_long_range_B_refined3.58982
X-RAY DIFFRACTIONr_long_range_B_other2.9558622
X-RAY DIFFRACTIONr_rigid_bond_restr6.58937607
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.188 26911 -
obs--95.41 %

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