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- PDB-7bjk: Crystal structure of the chloroplastic Fe superoxide dismutase PA... -

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Basic information

Entry
Database: PDB / ID: 7bjk
TitleCrystal structure of the chloroplastic Fe superoxide dismutase PAP9 from Arabidopsis thaliana.
ComponentsSuperoxide dismutase [Fe] 2, chloroplastic
KeywordsOXIDOREDUCTASE / Iron superoxide dismutase / chloroplast
Function / homology
Function and homology information


chloroplast nucleoid / chloroplast thylakoid / thylakoid / superoxide dismutase / superoxide dismutase activity / response to UV / chloroplast / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Superoxide dismutase [Fe] 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCobessi, D. / Blanvillain, R. / Pfannschmidt, T.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0031 France
CitationJournal: Front Plant Sci / Year: 2021
Title: The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features.
Authors: Favier, A. / Gans, P. / Boeri Erba, E. / Signor, L. / Muthukumar, S.S. / Pfannschmidt, T. / Blanvillain, R. / Cobessi, D.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Fe] 2, chloroplastic
B: Superoxide dismutase [Fe] 2, chloroplastic
C: Superoxide dismutase [Fe] 2, chloroplastic
D: Superoxide dismutase [Fe] 2, chloroplastic
E: Superoxide dismutase [Fe] 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,74310
Polymers154,4165
Non-polymers3275
Water7,188399
1
A: Superoxide dismutase [Fe] 2, chloroplastic
B: Superoxide dismutase [Fe] 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8974
Polymers61,7662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-7 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Superoxide dismutase [Fe] 2, chloroplastic
D: Superoxide dismutase [Fe] 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8974
Polymers61,7662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-6 kcal/mol
Surface area19680 Å2
MethodPISA
3
E: Superoxide dismutase [Fe] 2, chloroplastic
hetero molecules

E: Superoxide dismutase [Fe] 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8974
Polymers61,7662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y,-z+21
Buried area1780 Å2
ΔGint-6 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.090, 83.010, 118.240
Angle α, β, γ (deg.)90.000, 115.759, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-487-

HOH

21E-409-

HOH

31E-462-

HOH

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Components

#1: Protein
Superoxide dismutase [Fe] 2, chloroplastic / Protein ALBINO OR PALE GREEN 8 / Protein FE SUPEROXIDE DISMUTASE 2


Mass: 30883.131 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FSD2, APG8, At5g51100, MWD22.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LU64, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 from 15 to 19 %, 0.1 M BisTris pH 6.5, 0.2 M NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→48.2 Å / Num. obs: 83998 / % possible obs: 94.5 % / Redundancy: 3.82 % / Biso Wilson estimate: 37.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.87
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 5642 / CC1/2: 0.605 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UNF

1unf


Resolution: 2.25→48.2 Å / SU ML: 0.3014 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 4080 4.86 %
Rwork0.1794 79860 -
obs0.1814 83940 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.82 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8593 0 5 399 8997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718848
X-RAY DIFFRACTIONf_angle_d0.89412044
X-RAY DIFFRACTIONf_chiral_restr0.05361274
X-RAY DIFFRACTIONf_plane_restr0.00591542
X-RAY DIFFRACTIONf_dihedral_angle_d15.67853139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.38111230.33962506X-RAY DIFFRACTION86.37
2.28-2.30.32251200.31642508X-RAY DIFFRACTION85.91
2.3-2.330.31551340.29262461X-RAY DIFFRACTION86.18
2.33-2.360.30031540.27112720X-RAY DIFFRACTION93.89
2.36-2.40.34611320.27092819X-RAY DIFFRACTION96.72
2.4-2.430.2891290.26032781X-RAY DIFFRACTION96.49
2.43-2.470.35111290.26032783X-RAY DIFFRACTION96.07
2.47-2.510.31631520.26232796X-RAY DIFFRACTION96.18
2.51-2.550.29261280.25732811X-RAY DIFFRACTION96.17
2.55-2.590.32371550.25052766X-RAY DIFFRACTION96.34
2.59-2.640.29821260.24082780X-RAY DIFFRACTION95.84
2.64-2.690.26921550.25022774X-RAY DIFFRACTION95.47
2.69-2.740.27751410.22942754X-RAY DIFFRACTION94.64
2.74-2.80.28031390.20812752X-RAY DIFFRACTION95.76
2.8-2.870.23921460.18992802X-RAY DIFFRACTION95.56
2.87-2.940.22371530.17962755X-RAY DIFFRACTION95.75
2.94-3.020.23941300.19732799X-RAY DIFFRACTION95.69
3.02-3.110.27851480.20062784X-RAY DIFFRACTION95.41
3.11-3.210.25031600.20342782X-RAY DIFFRACTION96.08
3.21-3.320.21741330.20242751X-RAY DIFFRACTION95.53
3.32-3.460.20141420.17382797X-RAY DIFFRACTION95.55
3.46-3.610.21741360.16042801X-RAY DIFFRACTION95.48
3.61-3.80.20691510.15842793X-RAY DIFFRACTION96.08
3.8-4.040.19531570.14752750X-RAY DIFFRACTION95.69
4.04-4.350.15441360.12772826X-RAY DIFFRACTION95.89
4.35-4.790.14871430.11232802X-RAY DIFFRACTION95.4
4.79-5.480.17851580.1232784X-RAY DIFFRACTION95.18
5.48-6.910.19291330.15292828X-RAY DIFFRACTION95.03
6.91-48.20.1661370.15362795X-RAY DIFFRACTION92.23

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