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- PDB-8jd8: Crystal structure of Citrus limon Cu-Zn superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 8jd8
TitleCrystal structure of Citrus limon Cu-Zn superoxide dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / superoxide dismutase / Citrus limon
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCitrus limon (lemon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsUtami, R.A. / Yoshida, H. / Retnoningrum, D.S. / Ismaya, W.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Direct relationship between dimeric form and activity in the acidic copper-zinc superoxide dismutase from lemon.
Authors: Utami, R.A. / Yoshida, H. / Kartadinata, L.H. / Abdillah, V.A. / Faratilla, C.R. / Retnoningrum, D.S. / Ismaya, W.T.
History
DepositionMay 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,06713
Polymers67,4864
Non-polymers5819
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-121 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.111, 74.554, 61.686
Angle α, β, γ (deg.)90.00, 106.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 16871.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus limon (lemon) / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q71S31, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Magnesium chloride, Calcium chloride, Imidazole, MES, PEG500 MME, PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→49.36 Å / Num. obs: 44510 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.044 / Rrim(I) all: 0.081 / Χ2: 0.47 / Net I/σ(I): 9.3
Reflection shellResolution: 1.86→1.9 Å / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.436 / Num. measured all: 9125 / Num. unique obs: 2740 / CC1/2: 0.862 / Rpim(I) all: 0.28 / Rrim(I) all: 0.52 / Χ2: 0.46 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
REFMAC5.8refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2L

2q2l


Resolution: 1.86→49.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.026 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26598 2210 5 %RANDOM
Rwork0.17296 ---
obs0.17752 42281 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å21.03 Å2
2---2.09 Å2-0 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.86→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 9 177 4454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134352
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173866
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.6375918
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5849036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8215608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7524.725182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64115616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0911512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025140
X-RAY DIFFRACTIONr_gen_planes_other00.02776
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_it4.0892.4062444
X-RAY DIFFRACTIONr_mcbond_other4.0872.4052442
X-RAY DIFFRACTIONr_mcangle_it4.8853.6273048
X-RAY DIFFRACTIONr_mcangle_other4.8843.6273048
X-RAY DIFFRACTIONr_scbond_it5.3762.7571908
X-RAY DIFFRACTIONr_scbond_other5.3762.7571908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2173.9812870
X-RAY DIFFRACTIONr_long_range_B_refined6.58330.5394510
X-RAY DIFFRACTIONr_long_range_B_other6.55430.4734484
X-RAY DIFFRACTIONr_rigid_bond_restr8.56838218
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 166 -
Rwork0.202 3092 -
obs--99.88 %

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