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- PDB-8yu5: The structure of non-activated thiocyanate dehydrogenase mutant w... -

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Basic information

Entry
Database: PDB / ID: 8yu5
TitleThe structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q)
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / pmTcDH H447Q / Point mutation in the active center / Trinuclear copper center / Pelomicrobium methylotrophicum
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 / DI(HYDROXYETHYL)ETHER / Twin-arginine translocation signal domain-containing protein
Similarity search - Component
Biological speciesPelomicrobium methylotrophicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsVarfolomeeva, L.A. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q)
Authors: Varfolomeeva, L.A. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,99815
Polymers108,1672
Non-polymers83213
Water18,8081044
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-74 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.770, 96.440, 147.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54083.285 Da / Num. of mol.: 2 / Mutation: H447Q
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

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Non-polymers , 5 types, 1057 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1M 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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 164827 / % possible obs: 97.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Net I/σ(I): 19.01
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.45-1.50.56155220.8650.6091
1.5-1.60.377256120.9570.4071
1.6-1.70.249202030.980.2691
1.7-1.80.165159870.9910.1781
1.8-1.90.118128300.9950.1281
1.9-2.020.086123210.9960.0931
2.02-2.150.07104680.9970.0761
2.15-2.320.062104190.9970.0671
2.32-2.540.05497500.9970.0581
2.54-2.840.04988450.9980.0531
2.84-3.280.04478120.9980.0481
3.28-40.03966320.9990.0421
4-100.03578300.9990.0381
10-500.0285960.9990.031

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.88 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.902 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17314 8215 5 %RANDOM
Rwork0.14958 ---
obs0.15074 156611 97.55 %-
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: 16.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å20 Å2
2---0.03 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.45→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 35 1044 8315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0127618
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.64310334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45222.101357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.465151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0331540
X-RAY DIFFRACTIONr_chiral_restr0.1340.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025777
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_it1.3011.3473762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8052.0244703
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1723856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.72720.07411793
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: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 600 -
Rwork0.256 11280 -
obs--96.15 %

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