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- PDB-8you: The pmTcDH complex structure with an inhibitor SeCN -

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Basic information

Entry
Database: PDB / ID: 8you
TitleThe pmTcDH complex structure with an inhibitor SeCN
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / Pelomicrobium methylotrophicum / Substrate analogue / Inhibitor / Complex / TcDH / trinuclear copper center / selenocyanate / SeCN
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 / SELENIUM ATOM / SELENOCYANATE ION / Twin-arginine translocation signal domain-containing protein
Similarity search - Component
Biological speciesPelomicrobium methylotrophicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVarfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMar 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: 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)108,93013
Polymers108,1872
Non-polymers74411
Water15,313850
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-130 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.030, 96.670, 147.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 861 molecules

#2: Chemical ChemComp-SEK / SELENOCYANATE ION


Mass: 104.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Se / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 44.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 86192 / % possible obs: 96.5 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.087 / Net I/σ(I): 12.22
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.850.98767450.7581.131
1.85-1.90.67661460.8580.7781
1.9-20.366103710.940.4231
2-2.10.21185240.9650.2441
2.1-2.150.15436640.9750.1781
2.15-2.320.119102110.9830.1381
2.32-2.540.08591060.9880.0991
2.54-2.840.07383010.9920.0821
2.84-3.280.0679760.9950.0681
3.28-40.05366980.9950.0591
4-100.05179020.9940.0581
10-500.0695480.9860.081

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.262 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23533 4386 5.1 %RANDOM
Rwork0.18877 ---
obs0.19116 81806 96.48 %-
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: 21.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7271 0 18 850 8139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0127493
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.63910185
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8165935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56122.12349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.487151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3411538
X-RAY DIFFRACTIONr_chiral_restr0.1580.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.025732
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2361.9383747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7342.8934679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1783746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.81927.75112006
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr33.15234
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.865 335 -
Rwork0.881 6042 -
obs--97.61 %

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