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- PDB-1xso: THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DI... -

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Entry
Database: PDB / ID: 1xso
TitleTHREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROMS RESOLUTION
ComponentsCOPPER,ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
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] B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.49 Å
AuthorsDjinovic Carugo, K. / Coda, A. / Battistoni, A. / Carri, M.T. / Polticelli, F. / Desideri, A. / Rotilio, G. / Wilson, K.S. / Bolognesi, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution.
Authors: Djinovic Carugo, K. / Battistoni, A. / Carri, M.T. / Polticelli, F. / Desideri, A. / Rotilio, G. / Coda, A. / Wilson, K.S. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Conserved Patterns in the Cu,Zn Superoxide Dismutase Family
Authors: Bordo, D. / Djinovic, K. / Bolognesi, K.M.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallographic Study of Azide-Inhibited Bovine Cu,Zn Superoxide Dismutase
Authors: Djinovic Carugo, K. / Polticelli, K.F. / Desideri, A. / Rotilio, G. / Wilson, K.S. / Bolognesi, M.
#3: Journal: FEBS Lett. / Year: 1994
Title: Crystal Structure of the Cyanide-Inhibited Xenopus Laevis Cu,Zn Superoxide Dismutase at 98 K
Authors: Djinovic Carugo, K. / Battistoni, K.A. / Carri, M.T. / Polticelli, F. / Desideri, A. / Rotilio, G. / Coda, A. / Bolognesi, M.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1993
Title: Crystallisation and Preliminary Crystallographic Analysis of Recombinant Xenopus Laevis Cu,Zn Superoxide Dismutase B
Authors: Djinovic Carugo, K. / Collyer, K.C. / Coda, A. / Carri, M.T. / Battistoni, A. / Botaro, G. / Polticelli, F. / Desideri, A. / Bolognesi, M.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal Structure of Yeast Cu,Zn Superoxide Dismutase
Authors: Djinovic, K. / Gatti, G. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Marmocchi, F. / Rotilio, G. / Bolognesi, M.
History
DepositionMar 14, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: computing / software / Item: _computing.structure_refinement
Revision 1.5Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_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.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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: COPPER,ZINC SUPEROXIDE DISMUTASE
B: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8726
Polymers30,6142
Non-polymers2584
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-39 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.450, 68.940, 58.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.98783, -0.01029, -0.15522), (-0.00836, -0.99988, 0.01307), (-0.15533, -0.01161, -0.98779)
Vector: 1.43777, 33.15571, 17.07902)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. A 151 B 2 .. B 151 0.279 CALCULATED FOR C-ALPHA ATOMS

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Components

#1: Protein COPPER,ZINC SUPEROXIDE DISMUTASE


Mass: 15306.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PKK233-2 TRC PROMOTER / Production host: Escherichia coli (E. coli) / References: UniProt: P15107, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 350 / 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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal grow
*PLUS
Temperature: 301 K / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218 %(w/v)PEG40001reservoir
30.05 Msodium phosphate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: CUSTOM-MADE / Detector: IMAGE PLATE / Date: Aug 18, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 49209 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.98 % / Rmerge(I) obs: 0.078
Reflection
*PLUS
Highest resolution: 1.49 Å / Num. measured all: 245181 / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
SHELXL-93refinement
PROLSQrefinement
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 1.49→10 Å / σ(F): 0 / Details: RESIDUE 24 IS IN POOR ELECTRON DENSITY.
RfactorNum. reflection
Rfree0.169 -
Rwork0.104 -
obs0.104 49209
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 1.49→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 4 350 2541
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.583
X-RAY DIFFRACTIONx_mcangle_it3.534
X-RAY DIFFRACTIONx_scbond_it6.525
X-RAY DIFFRACTIONx_scangle_it8.926
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.03
X-RAY DIFFRACTIONx_planar_d0.050.04
X-RAY DIFFRACTIONx_plane_restr0.020.025
X-RAY DIFFRACTIONx_chiral_restr0.150.288

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