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- PDB-8bpn: The structure of thiocyanate dehydrogenase mutant form with Phe 4... -

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Basic information

Entry
Database: PDB / ID: 8bpn
TitleThe structure of thiocyanate dehydrogenase mutant form with Phe 436 replaced by Gln from Thioalkalivibrio paradoxus
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / Copper containing enzyme / Mutant form / Substitution in the active center / Thioalkalivibrio paradoxus
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 / DI(HYDROXYETHYL)ETHER / Twin-arginine translocation signal domain-containing protein
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsVarfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Kulikova, O.G. / Dergousova, N.I. / Rakitina, T.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation20-14-00314 Russian Federation
CitationJournal: Crystals / Year: 2022
Title: Probing the Role of a Conserved Phenylalanine in the Active Site of Thiocyanate Dehydrogenase
Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Kulikova, O.G. / Dergousova, N.I. / Rakitina, T.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionJan 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)220,65514
Polymers219,9354
Non-polymers72110
Water7,638424
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)110,4348
Polymers109,9672
Non-polymers4666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-76 kcal/mol
Surface area28130 Å2
MethodPISA
2
C: Twin-arginine translocation signal domain-containing protein
D: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2216
Polymers109,9672
Non-polymers2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-83 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.559, 162.122, 90.861
Angle α, β, γ (deg.)90.00, 119.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 54983.652 Da / Num. of mol.: 4 / Mutation: F436Q
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2 M DL-Malic acid, pH 7.0, 20% w/v Polyethylene glycol 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: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→81.06 Å / Num. obs: 143470 / % possible obs: 93.9 % / Redundancy: 4.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.064 / Rrim(I) all: 0.134 / Χ2: 0.96 / Net I/σ(I): 7.3 / Num. measured all: 611643
Reflection shellResolution: 2→2.03 Å / % possible obs: 95.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.471 / Num. measured all: 31193 / Num. unique obs: 7191 / CC1/2: 0.837 / Rpim(I) all: 0.25 / Rrim(I) all: 0.534 / Χ2: 0.94 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OEX

5oex


Resolution: 1.99→81.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.673 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21398 6911 4.8 %RANDOM
Rwork0.17357 ---
obs0.17554 136401 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.341 Å2
Baniso -1Baniso -2Baniso -3
1--6.07 Å2-0 Å2-4.34 Å2
2--15.76 Å20 Å2
3----9.69 Å2
Refinement stepCycle: 1 / Resolution: 1.99→81.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14512 0 22 424 14958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01214964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.63620394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.31451864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94223.287721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.528152317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5361564
X-RAY DIFFRACTIONr_chiral_restr0.1620.21910
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211560
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_it3.5982.1477468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3213.2069328
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2882.3097496
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.17529.31422703
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A155030.09
12B155030.09
21A156130.08
22C156130.08
31A154610.09
32D154610.09
41B155300.09
42C155300.09
51B155500.08
52D155500.08
61C154890.09
62D154890.09
LS refinement shellResolution: 1.993→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 527 -
Rwork0.186 8687 -
obs--80.62 %

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