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- PDB-6g50: The structure of thiocyanate dehydrogenase from Thioalkalivibrio ... -

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Basic information

Entry
Database: PDB / ID: 6g50
TitleThe structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.
ComponentsUncharacterized protein
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 / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsPolyakov, K.M. / Tsallagov, S.I. / Tikhkonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science FoundationGrant 14-24-00172 Russian Federation
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
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
SupersessionAug 14, 2019ID: 5F30
Revision 1.1Aug 14, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr / reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.2Jul 22, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,69229
Polymers206,8494
Non-polymers1,84325
Water27,5811531
1
A: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,21813
Polymers103,4242
Non-polymers79411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-159 kcal/mol
Surface area28500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-324 kcal/mol
Surface area55570 Å2
MethodPISA
3
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,47416
Polymers103,4242
Non-polymers1,04914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-170 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 162.280, 90.570
Angle α, β, γ (deg.)90.00, 119.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 51712.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio paradoxus ARh 1 (bacteria)
References: UniProt: W0DP94
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1531 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PRECIPITANT SOLUTION: 0.2 M lithium sulfate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v PEG 3350. Protein solution: TcDH 10 mg/ml 25 mM borate, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.551
11L, -K, H20.449
ReflectionResolution: 1.65→45.4 Å / Num. obs: 691361 / % possible obs: 97.3 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rrim(I) all: 0.098 / Net I/av σ(I): 9.2 / Net I/σ(I): 9.2
Reflection shellResolution: 1.65→1.7 Å / Mean I/σ(I) obs: 1.65 / Num. unique obs: 22515 / CC1/2: 0.51 / Rrim(I) all: 0.79 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5F30

5f30
PDB Unreleased entry


Resolution: 1.65→45.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.978 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.019
RfactorNum. reflection% reflectionSelection details
Rfree0.20716 26618 10 %RANDOM
Rwork0.14261 ---
obs0.14699 238854 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.444 Å2
Baniso -1Baniso -2Baniso -3
1--4.43 Å2-0 Å2-0.36 Å2
2--8.37 Å20 Å2
3----3.95 Å2
Refinement stepCycle: 1 / Resolution: 1.65→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14572 0 69 1531 16172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01915207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.94420729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.86251878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26824.457682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.413152403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4941570
X-RAY DIFFRACTIONr_chiral_restr0.1330.22247
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111678
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_it1.4071.7497503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9392.6259380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98236.767704
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.12125.71224820
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free12.75651
X-RAY DIFFRACTIONr_sphericity_bonded10.83153
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 14118 -
Rwork0.221 4859 -
obs--94.3 %

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