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- PDB-3mnd: Crystallographic analysis of the cystosolic cu/zn Superoxide dism... -

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Basic information

Entry
Database: PDB / ID: 3mnd
TitleCrystallographic analysis of the cystosolic cu/zn Superoxide dismutase from taenia solium
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / CU/ZN-SUPEROXIDE DISMUTASE / METAL-MEDIATED SELF-ASSEMBLY
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding / identical protein binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesTaenia solium (pork tapeworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHernandez-Santoyo, A. / Rodriguez-Romero, A.
Citation
Journal: Febs J. / Year: 2011
Title: Crystal structure of Cu / Zn superoxide dismutase from Taenia solium reveals metal-mediated self-assembly
Authors: Hernandez-Santoyo, A. / Landa, A. / Gonzalez-Mondragon, E. / Pedraza-Escalona, M. / Parra-Unda, R. / Rodriguez-Romero, A.
#1: Journal: Int.J.Parasitol. / Year: 2002
Title: Cloning, production and characterisation of a recombinant Cu/Zn superoxide dismutase from Taenia solium.
Authors: Castellanos-Gonzalez, A. / Jimenez, L. / Landa, A.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,86511
Polymers31,2272
Non-polymers6389
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-121 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.171, 53.798, 117.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15613.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM / Source: (gene. exp.) Taenia solium (pork tapeworm) / Strain: MEXICAN STRAIN / Plasmid: PRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8WRF5, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 20% w/v polyethylene glycol monomethyl ether 2,000, in hexahydrate 0.1 M Tris buffer pH 8.5 and 0.01 M Nickel (II) chloridE., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2005 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→39.64 Å / Num. obs: 13829 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.94 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7
Reflection shellHighest resolution: 2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TO4

1to4


Resolution: 2.2→39.64 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1384 10.01 %
Rwork0.192 --
obs0.198 13829 97.7 %
all-7742 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.96 Å2 / ksol: 0.38 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 19 109 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072255
X-RAY DIFFRACTIONf_angle_d1.0823036
X-RAY DIFFRACTIONf_dihedral_angle_d14.548790
X-RAY DIFFRACTIONf_chiral_restr0.07334
X-RAY DIFFRACTIONf_plane_restr0.003407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27870.29521330.21391197X-RAY DIFFRACTION96
2.2787-2.36990.31091360.20071223X-RAY DIFFRACTION98
2.3699-2.47770.27221360.19691217X-RAY DIFFRACTION98
2.4777-2.60830.27231360.20571230X-RAY DIFFRACTION98
2.6083-2.77170.25781360.20711226X-RAY DIFFRACTION98
2.7717-2.98570.30931380.21371240X-RAY DIFFRACTION98
2.9857-3.2860.26121380.18981243X-RAY DIFFRACTION98
3.286-3.76120.23761400.18151256X-RAY DIFFRACTION98
3.7612-4.73740.19871400.16371265X-RAY DIFFRACTION98
4.7374-39.64630.22151510.19791348X-RAY DIFFRACTION98

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