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- PDB-8z76: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -

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Basic information

Entry
Database: PDB / ID: 8z76
TitleThe structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 during 6 months
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / Copper enzyme / Activation by crystals soaking / Copper incorporation in the active site / Trinuclear copper center / Conformational changes in a crystal
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 / 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. / Solovieva, A.Y. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Crystallography Reports / Year: 2025
Title: Effect of Copper Ions on the Crystal Packing and Conformation of Thiocyanate Dehydrogenase in the Crystal Structure
Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Dergousova, N.I. / Minyaev, M.E. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 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.title / _citation.year / _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
C: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,24919
Polymers162,2803
Non-polymers96916
Water14,430801
1
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)108,90314
Polymers108,1872
Non-polymers71612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-110 kcal/mol
Surface area28800 Å2
MethodPISA
2
C: Twin-arginine translocation signal domain-containing protein
hetero molecules

C: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69210
Polymers108,1872
Non-polymers5058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
Buried area5210 Å2
ΔGint-101 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 101.750, 276.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-825-

HOH

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Components

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


Mass: 54093.301 Da / Num. of mol.: 3
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 20% PEG 8000, 8% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 125833 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.11 / Net I/σ(I): 12.69
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.851.12698190.6791.2171
1.85-1.90.91987660.7780.9931
1.9-2.020.597176720.9060.6451
2.02-2.150.409151010.9590.4431
2.15-2.320.28150210.9770.3041
2.32-2.540.192139860.9860.211
2.54-2.840.129127800.9930.141
2.84-3.280.083112730.9960.091
3.28-40.05994990.9970.0641
4-100.046111000.9980.051
10-500.0338160.9980.0361

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8Q9X

8q9x


Resolution: 1.8→47.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.198 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21728 6278 5 %RANDOM
Rwork0.1675 ---
obs0.16994 119555 98.78 %-
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: 29.113 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å2-0 Å2
2--2.11 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 31 801 11632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01211132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2611.63915177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78351395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36522.441512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.338151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8911551
X-RAY DIFFRACTIONr_chiral_restr0.1690.21439
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.028541
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_it3.4062.7875586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0154.1576979
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2482.985546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.01617535
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
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
Rfree0.335 449 -
Rwork0.299 8716 -
obs--98.15 %

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