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- PDB-3mkg: Low pH as-isolated tomato chloroplast superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 3mkg
TitleLow pH as-isolated tomato chloroplast superoxide dismutase
ComponentsSuperoxide dismutase [Cu-Zn], chloroplastic
KeywordsOXIDOREDUCTASE / TOMATO CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / CHLOROPLAST / DISULFIDE BOND / 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
Superoxide dismutase [Cu-Zn], chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionApr 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4204
Polymers31,2892
Non-polymers1312
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-87 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.993, 104.798, 35.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15644.372 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1 M lithium chloride, 0.1 M citric acid, 20% PEG 6000, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13134 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.116 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1270 / Rsym value: 0.468 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3HOG

3hog


Resolution: 2.2→31.451 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 644 4.92 %random
Rwork0.2143 ---
obs0.2165 13082 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.211 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.2803 Å20 Å20 Å2
2---4.8233 Å20 Å2
3----0.3831 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 2 75 1831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081775
X-RAY DIFFRACTIONf_angle_d1.122421
X-RAY DIFFRACTIONf_dihedral_angle_d16.263611
X-RAY DIFFRACTIONf_chiral_restr0.066299
X-RAY DIFFRACTIONf_plane_restr0.004324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.36620.26081390.21892404X-RAY DIFFRACTION99
2.3662-2.60420.29671210.22732449X-RAY DIFFRACTION100
2.6042-2.98080.27771310.22852470X-RAY DIFFRACTION100
2.9808-3.75450.241160.19752494X-RAY DIFFRACTION100
3.7545-31.4540.24261370.20632621X-RAY DIFFRACTION100

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