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- PDB-5oex: Complex with iodine ion for thiocyanate dehydrogenase from Thioal... -

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Basic information

Entry
Database: PDB / ID: 5oex
TitleComplex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus
ComponentsTHIOCYANATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THIOCYANATE DEHYDROGENASE / COPPER CENTERS
Function / homology
Function and homology information


Cytochrome 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
Similarity search - Domain/homology
COPPER (II) ION / IODIDE ION / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Twin-arginine translocation signal domain-containing protein
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPolyakov, K.M. / Tsallagov, S.I. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Fondation15-14-00063 Russian Federation
CitationJournal: To Be Published
Title: Discovery and characterization of a novel copper containing enzyme - THIOCYANATE DEHYDROGENASE.
Authors: Tikhonova, T.V. / Sorokin, D.I. / Tsallagov, S.I. / Polyakov, K.M. / Trofimov, A.A. / Shabalin, I.G. / Khrenova, M.G. / Muyser, G. / Rakitina, T.V. / Popov, V.O.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionAug 1, 2018ID: 5F30
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Jan 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.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: THIOCYANATE DEHYDROGENASE
B: THIOCYANATE DEHYDROGENASE
C: THIOCYANATE DEHYDROGENASE
D: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,25832
Polymers206,8494
Non-polymers2,40928
Water16,556919
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16850 Å2
ΔGint-253 kcal/mol
Surface area54790 Å2
2
A: THIOCYANATE DEHYDROGENASE
B: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,69017
Polymers103,4242
Non-polymers1,26615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-119 kcal/mol
Surface area28440 Å2
MethodPISA
3
C: THIOCYANATE DEHYDROGENASE
D: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56715
Polymers103,4242
Non-polymers1,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-133 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.820, 159.450, 91.000
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
THIOCYANATE DEHYDROGENASE


Mass: 51712.160 Da / Num. of mol.: 4
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) / Variant (production host): Star / References: UniProt: W0DP94

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Non-polymers , 6 types, 947 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PROTEIN SOLUTION: 10 MG/ML PROTEIN, 25 MM BORATE BUFFER (PH 9.5). PRECIPITANT SOLUTION: 0.025 M AMMONIUM IODIDE, 20.0 % W/V PEG 3350. VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 124180 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / CC1/2: 0.996 / Rpim(I) all: 0.155 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.35 / Num. unique obs: 9243 / CC1/2: 0.764 / Rpim(I) all: 0.861 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F30

5f30
PDB Unreleased entry


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.97 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.19841 6102 4.9 %RANDOM
Rwork0.15573 ---
obs0.15784 118078 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.47 Å2
2---1.02 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14572 0 52 919 15543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.94220529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32251869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27524.456671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.593152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461570
X-RAY DIFFRACTIONr_chiral_restr0.1430.22225
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111598
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_it1.6521.9377474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3442.8959337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9082.1717608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.3679.20624141
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 403 -
Rwork0.261 8827 -
obs--94.39 %

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