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- PDB-3s0p: Copper-reconstituted Tomato Chloroplast Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 3s0p
TitleCopper-reconstituted Tomato Chloroplast Superoxide Dismutase
ComponentsSuperoxide dismutase [Cu-Zn], chloroplastic
KeywordsOXIDOREDUCTASE / ANTIOXIDANT / METAL-BINDING / CHLOROPLAST / TRANSIT PEPTIDE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / chloroplast / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn], chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGalaleldeen, A. / Taylor, A.B. / Hart, P.J.
CitationJournal: To be Published
Title: Biophysical properties of Tomato Chloroplast SOD
Authors: Galaleldeen, A. / Taylor, A.B. / Hart, P.J.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn], chloroplastic
B: Superoxide dismutase [Cu-Zn], chloroplastic
C: Superoxide dismutase [Cu-Zn], chloroplastic
D: Superoxide dismutase [Cu-Zn], chloroplastic
E: Superoxide dismutase [Cu-Zn], chloroplastic
F: Superoxide dismutase [Cu-Zn], chloroplastic
G: Superoxide dismutase [Cu-Zn], chloroplastic
H: Superoxide dismutase [Cu-Zn], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,66316
Polymers125,1558
Non-polymers5088
Water00
1
A: Superoxide dismutase [Cu-Zn], chloroplastic
B: Superoxide dismutase [Cu-Zn], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers31,2892
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-36 kcal/mol
Surface area11210 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn], chloroplastic
D: Superoxide dismutase [Cu-Zn], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers31,2892
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-36 kcal/mol
Surface area11210 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn], chloroplastic
F: Superoxide dismutase [Cu-Zn], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers31,2892
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-36 kcal/mol
Surface area11170 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn], chloroplastic
H: Superoxide dismutase [Cu-Zn], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4164
Polymers31,2892
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-36 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.866, 105.329, 69.660
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
211chain B and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
311chain C and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
411chain D and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
511chain E and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
611chain F and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
711chain G and (resseq 2:65 or resseq 81:124 or resseq 142:154 )
811chain H and (resseq 2:65 or resseq 81:124 or resseq 142:154 )

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Components

#1: Protein
Superoxide dismutase [Cu-Zn], chloroplastic


Mass: 15644.372 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: SODCP.2 / Plasmid: PAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14831, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu

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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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1M Lithium Sulfate, 25% PEG 6000, 0.1 M citric Acid, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Feb 11, 2011
RadiationMonochromator: Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 19257 / % possible obs: 99.8 % / Observed criterion σ(I): 5.4 / Redundancy: 3.7 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.144 / Net I/σ(I): 2.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1917 / Rsym value: 0.377 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MKG

3mkg


Resolution: 3→24.723 Å / SU ML: 0.43 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 982 5.11 %random
Rwork0.2036 ---
obs0.206 19225 99.53 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.148 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-15.5159 Å20 Å2-0.7642 Å2
2--2.0844 Å20 Å2
3---1.1091 Å2
Refinement stepCycle: LAST / Resolution: 3→24.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 8 0 7021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177108
X-RAY DIFFRACTIONf_angle_d1.4379686
X-RAY DIFFRACTIONf_dihedral_angle_d15.9332454
X-RAY DIFFRACTIONf_chiral_restr0.0841195
X-RAY DIFFRACTIONf_plane_restr0.0071296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A865X-RAY DIFFRACTIONPOSITIONAL
12B865X-RAY DIFFRACTIONPOSITIONAL0.089
13C865X-RAY DIFFRACTIONPOSITIONAL0.104
14D865X-RAY DIFFRACTIONPOSITIONAL0.082
15E865X-RAY DIFFRACTIONPOSITIONAL0.076
16F865X-RAY DIFFRACTIONPOSITIONAL0.09
17G865X-RAY DIFFRACTIONPOSITIONAL0.091
18H865X-RAY DIFFRACTIONPOSITIONAL0.088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.1560.34931330.28542581X-RAY DIFFRACTION98
3.156-3.35330.33151460.25232580X-RAY DIFFRACTION100
3.3533-3.61150.30211270.24552608X-RAY DIFFRACTION100
3.6115-3.97360.2421390.20562616X-RAY DIFFRACTION100
3.9736-4.54550.20371360.16672607X-RAY DIFFRACTION100
4.5455-5.71510.20731360.16092631X-RAY DIFFRACTION100
5.7151-24.72340.22051650.19052620X-RAY DIFFRACTION99

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