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- PDB-7sbh: Crystal structure of the iron superoxide dismutase from Acinetoba... -

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Basic information

Entry
Database: PDB / ID: 7sbh
TitleCrystal structure of the iron superoxide dismutase from Acinetobacter sp. Ver3
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / metalloenzyme / extremophile / oxidative stress
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
: / FLAVIN MONONUCLEOTIDE / Superoxide dismutase
Similarity search - Component
Biological speciesAcinetobacter sp. Ver3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsSteimbruch, B.A. / Albanesi, D. / Repizo, G.D. / Lisa, M.N.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2015-1492 Argentina
CitationJournal: Sci Rep / Year: 2022
Title: The distinctive roles played by the superoxide dismutases of the extremophile Acinetobacter sp. Ver3.
Authors: Steimbruch, B.A. / Sartorio, M.G. / Cortez, N. / Albanesi, D. / Lisa, M.N. / Repizo, G.D.
History
DepositionSep 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4073
Polymers22,8951
Non-polymers5122
Water6,341352
1
A: Superoxide dismutase
hetero molecules

A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8136
Polymers45,7892
Non-polymers1,0244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)70.933, 87.016, 75.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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Components

#1: Protein Superoxide dismutase /


Mass: 22894.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. Ver3 (bacteria) / Gene: CL42_08295 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A031LR83, superoxide dismutase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22 % w/v PEG 8000, 100 mM sodium cacodylate pH 7.5, 200 mM magnesium acetate, 1 mM flavin mononucleotide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.34→28.54 Å / Num. obs: 51999 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 18.9
Reflection shellResolution: 1.34→1.37 Å / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2402 / CC1/2: 0.705 / Rpim(I) all: 0.36 / Rrim(I) all: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISA

1isa


Resolution: 1.34→27.49 Å / SU ML: 0.1066 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.3154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1624 2618 5.04 %
Rwork0.1444 49349 -
obs0.1452 51967 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 1.34→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 32 352 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181750
X-RAY DIFFRACTIONf_angle_d1.14662398
X-RAY DIFFRACTIONf_chiral_restr0.0946256
X-RAY DIFFRACTIONf_plane_restr0.009305
X-RAY DIFFRACTIONf_dihedral_angle_d15.2863608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.21961190.22372439X-RAY DIFFRACTION94.29
1.37-1.40.2251290.19732543X-RAY DIFFRACTION99.48
1.4-1.420.19271480.18472573X-RAY DIFFRACTION99.85
1.42-1.460.19691440.18412566X-RAY DIFFRACTION99.93
1.46-1.490.18631320.15752581X-RAY DIFFRACTION99.96
1.49-1.530.15691450.1472571X-RAY DIFFRACTION100
1.53-1.570.14331380.1372586X-RAY DIFFRACTION100
1.57-1.610.1331280.12982611X-RAY DIFFRACTION100
1.61-1.670.19331360.13462577X-RAY DIFFRACTION100
1.67-1.730.17151470.13862581X-RAY DIFFRACTION99.96
1.73-1.790.16571420.14442594X-RAY DIFFRACTION99.93
1.79-1.880.14841430.14332599X-RAY DIFFRACTION99.96
1.88-1.970.14591470.13842573X-RAY DIFFRACTION99.96
1.97-2.10.14651220.13032646X-RAY DIFFRACTION100
2.1-2.260.16561130.13392635X-RAY DIFFRACTION99.96
2.26-2.490.16091570.13842596X-RAY DIFFRACTION99.96
2.49-2.850.17381360.1542652X-RAY DIFFRACTION100
2.85-3.590.1571550.1422654X-RAY DIFFRACTION100
3.59-27.490.1561370.14092772X-RAY DIFFRACTION99.83

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