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- PDB-8q9x: The structure of thiocyanate dehydrogenase from Pelomicrobium met... -

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Basic information

Entry
Database: PDB / ID: 8q9x
TitleThe structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / copper enzyme / trinuclear copper center / atomic resolution / conformational changes / complex with molecular oxygen / Pelomicrobium methylotrophicum
Function / homologyNitrous 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 / COPPER (II) ION / OXYGEN MOLECULE / Twin-arginine translocation signal domain-containing protein
Function and homology information
Biological speciesPelomicrobium methylotrophicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsVarfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-30004 Russian Federation
CitationJournal: To Be Published
Title: Structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum at atomic resolution
Authors: Varfolomeeva, L.A. / Polyakov, K.M. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: 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)109,00314
Polymers108,1872
Non-polymers81712
Water23,7621319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-126 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.840, 96.570, 147.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54093.301 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 1319 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 441007 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Net I/σ(I): 14.21
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.05-1.10.808569970.7750.8751
1.1-1.150.518475530.8920.5631
1.15-1.20.379399790.940.4111
1.2-1.30.28627560.9680.3031
1.3-1.50.16808950.9890.1731
1.5-1.70.091473940.9950.0991
1.7-1.90.065295790.9970.0711
1.9-2.020.056125880.9970.061
2.02-2.150.052106410.9970.0561
2.15-2.320.049105760.9980.0531
2.32-2.540.04798670.9980.0511
2.54-2.840.04590260.9980.0491
2.84-3.280.04279530.9980.0451
3.28-40.03967100.9980.0421
4-100.03578920.9990.0381
10-500.0326010.9990.0361

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→45.93 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.578 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.12583 21961 5 %RANDOM
Rwork0.10846 ---
obs0.10933 419044 99.93 %-
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: 14.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.05→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 34 1319 8631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0127781
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166890
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.64310548
X-RAY DIFFRACTIONr_angle_other_deg0.8181.56115965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78822.291371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.903151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9571540
X-RAY DIFFRACTIONr_chiral_restr0.1290.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028660
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021710
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_it2.0783773
X-RAY DIFFRACTIONr_mcbond_other2.0783772
X-RAY DIFFRACTIONr_mcangle_it2.2094717
X-RAY DIFFRACTIONr_mcangle_other2.2094718
X-RAY DIFFRACTIONr_scbond_it2.2614008
X-RAY DIFFRACTIONr_scbond_other2.2584000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7625829
X-RAY DIFFRACTIONr_long_range_B_refined3.0198976
X-RAY DIFFRACTIONr_long_range_B_other2.7998664
X-RAY DIFFRACTIONr_rigid_bond_restr8.27737446
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 1621 -
Rwork0.213 30781 -
obs--99.82 %

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