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- PDB-8bhx: High resolution structure of the iron Superoxide Dismutase from T... -

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Basic information

Entry
Database: PDB / ID: 8bhx
TitleHigh resolution structure of the iron Superoxide Dismutase from Thermobifida fusca
ComponentsSuperoxide dismutase
KeywordsELECTRON TRANSPORT / iron Superoxide Dismutase / SOD / Thermobifida fusca / thermophilic bacteria / Reactive oxygen species (ROS).
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
BORIC ACID / : / Superoxide dismutase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLeiros, H.-K.S. / Sorlie, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Inorg.Chem. / Year: 2023
Title: Initial characterization of an iron superoxide dismutase from Thermobifida fusca.
Authors: Hamre, A.G. / Al-Sadawi, R. / Johannesen, K.M. / Bisarro, B. / Kjendseth, A.R. / Leiros, H.S. / Sorlie, M.
History
DepositionNov 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6555
Polymers45,4812
Non-polymers1743
Water13,565753
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules

A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,30910
Polymers90,9624
Non-polymers3476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14090 Å2
ΔGint-66 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.610, 58.590, 67.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-590-

HOH

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Components

#1: Protein Superoxide dismutase


Mass: 22740.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_0957 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) cells / References: UniProt: Q47RC2, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% (w/v) PEG 1500 and 0.1 M sodium malonate dibasic monohydrate, imidazole and boric acid buffer at pH 8.0, from a PACT premier screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→25 Å / Num. obs: 108003 / % possible obs: 98.79 % / Redundancy: 5.3 % / Biso Wilson estimate: 11.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0331 / Net I/av σ(I): 10.05 / Net I/σ(I): 10.05
Reflection shellResolution: 1.25→1.7 Å / Rmerge(I) obs: 0.3475 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 9675 / CC1/2: 0.673 / % possible all: 89.74

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSM

1bsm


Resolution: 1.25→24.65 Å / SU ML: 0.1153 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.4862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1445 2108 1.95 %
Rwork0.1254 105878 -
obs0.1258 107986 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.32 Å2
Refinement stepCycle: LAST / Resolution: 1.25→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 11 753 3965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883530
X-RAY DIFFRACTIONf_angle_d1.13264828
X-RAY DIFFRACTIONf_chiral_restr0.0862487
X-RAY DIFFRACTIONf_plane_restr0.0065644
X-RAY DIFFRACTIONf_dihedral_angle_d12.9505480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.29081440.28066190X-RAY DIFFRACTION87.75
1.28-1.310.26691430.25476713X-RAY DIFFRACTION95.37
1.31-1.350.23011500.22356983X-RAY DIFFRACTION98.77
1.35-1.390.21741280.18427062X-RAY DIFFRACTION99.71
1.39-1.430.15121370.15947091X-RAY DIFFRACTION99.99
1.43-1.480.17231440.14697070X-RAY DIFFRACTION99.97
1.48-1.540.16321380.1347113X-RAY DIFFRACTION100
1.54-1.610.13241640.12047065X-RAY DIFFRACTION99.96
1.61-1.70.14761370.11687109X-RAY DIFFRACTION99.94
1.7-1.80.13861270.11057139X-RAY DIFFRACTION99.97
1.8-1.940.13531370.11237156X-RAY DIFFRACTION99.99
1.94-2.140.12321320.10467185X-RAY DIFFRACTION100
2.14-2.450.11331480.10127199X-RAY DIFFRACTION100
2.45-3.080.14131290.10827291X-RAY DIFFRACTION100
3.08-24.650.12721500.11587512X-RAY DIFFRACTION99.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.916759556618-0.000748010497526-0.07901645388690.4507601522270.02125026856650.4520212087890.0116514474065-0.2053679050010.02179564218050.057637962324-0.0192336766264-0.03090207299460.01075373638570.04247466829640.01427815488110.0766522274535-0.0103207891984-0.006179467713140.113412940588-0.003482176267080.056827299925511.1810404634.3107830473189.2900362601
20.5574270326840.1005611235750.006215070131770.4775134327750.00108528394770.339408948183-0.01884848116930.0389118914210.00936852024606-0.03502399121040.0240570608163-0.0210256150103-0.0216435992360.0161334152334-0.002781795868990.0709609233607-0.00892118597450.005528061293270.05404510561690.0007583173921810.06654307085689.666534262897.0585585732760.0974909107
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 2 through 204)AA2 - 2031 - 216
22(chain 'B' and resid 2 through 204)BC2 - 2041 - 219

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