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- PDB-6sji: The structure of thiocyanate dehydrogenase from Thioalkalivibrio ... -

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Basic information

Entry
Database: PDB / ID: 6sji
TitleThe structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln
Componentsthiocyanate dehydrogenase
KeywordsOXIDOREDUCTASE / THIOCYANATE DEHYDROGENASE / COPPER CENTERS
Function / homologyCytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 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 / metal ion binding / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPolyakov, K.M. / Tikhonova, T.V. / Rakitina, T.V. / Osipov, E. / Popov, V.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase.
Authors: Tikhonova, T.V. / Sorokin, D.Y. / Hagen, W.R. / Khrenova, M.G. / Muyzer, G. / Rakitina, T.V. / Shabalin, I.G. / Trofimov, A.A. / Tsallagov, S.I. / Popov, V.O.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thiocyanate dehydrogenase
B: thiocyanate dehydrogenase
J: thiocyanate dehydrogenase
K: thiocyanate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,70616
Polymers207,8464
Non-polymers86012
Water21,3121183
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-211 kcal/mol
Surface area55740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.080, 160.410, 90.880
Angle α, β, γ (deg.)90.000, 98.114, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
thiocyanate dehydrogenase


Mass: 51961.461 Da / Num. of mol.: 4 / Mutation: Q482H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: THITH_13335 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0DP94
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17M Ammonium acetate, 0.085 M Sodium cacjdilate pH 6.5, 25.5 % v/v Polyatilen glycol 8000, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968623 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 176251 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / CC1/2: 0.987 / Rrim(I) all: 0.122 / Net I/σ(I): 6.63
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 13136 / CC1/2: 0.824 / Rrim(I) all: 0.456 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OEX

5oex


Resolution: 1.8→89.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.105 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1984 8761 -
Rwork0.1591 --
all0.161 --
obs-176251 96.253 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.112 Å20 Å2-1.128 Å2
2--0.176 Å20 Å2
3---0.032 Å2
Refinement stepCycle: LAST / Resolution: 1.8→89.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14585 0 24 1183 15792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01915094
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.94320558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44751869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67224.54674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.884152371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7391570
X-RAY DIFFRACTIONr_chiral_restr0.1450.22236
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111606
X-RAY DIFFRACTIONr_nbd_refined0.1970.213902
X-RAY DIFFRACTIONr_nbtor_refined0.3060.220452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.22420
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.225
X-RAY DIFFRACTIONr_mcbond_it1.8972.187482
X-RAY DIFFRACTIONr_mcangle_it2.5383.2599346
X-RAY DIFFRACTIONr_scbond_it3.01147.917611
X-RAY DIFFRACTIONr_scangle_it4.3363.53911211
X-RAY DIFFRACTIONr_lrange_it5.39431.58323540
X-RAY DIFFRACTIONr_sphericity_bonded16.62959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.8-1.8470.2726690.23125471351297.80940.229
1.847-1.8970.2366190.205122591317397.76060.208
1.897-1.9520.2346100.19118631278697.5520.192
1.952-2.0120.2315890.172116361248497.92530.174
2.012-2.0780.2196070.173111491203197.71420.176
2.078-2.1510.2095830.17106961168496.53370.171
2.151-2.2320.2315420.169103431122596.9710.166
2.232-2.3230.2365200.172100111087896.81010.167
2.323-2.4270.235000.17195711041896.66920.16
2.427-2.5450.2354690.1679128992596.69520.156
2.545-2.6830.2084170.178693944396.47360.158
2.683-2.8450.2044640.1648108896195.6590.152
2.845-3.0410.2213780.1697688843095.68210.164
3.041-3.2850.1973790.1577059782595.05430.159
3.285-3.5980.1723390.1416435719894.10950.15
3.598-4.0220.1613120.1335816653793.74330.147
4.022-4.6420.1412630.1175142579693.2540.131
4.642-5.6820.1442180.1334294487292.61080.151
5.682-8.0190.1841810.1573262380790.43870.17
8.019-89.970.1661020.1611790212888.90980.181

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