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- PDB-1sxz: Reduced bovine superoxide dismutase at pH 5.0 complexed with azide -

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Basic information

Entry
Database: PDB / ID: 1sxz
TitleReduced bovine superoxide dismutase at pH 5.0 complexed with azide
ComponentsPROTEIN (CU-ZN SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / SUPEROXIDE ACCEPTOR
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide / myeloid cell homeostasis / protein phosphatase 2B binding / Oxidoreductases; Acting on a sulfur group of donors ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide / myeloid cell homeostasis / protein phosphatase 2B binding / Oxidoreductases; Acting on a sulfur group of donors / auditory receptor cell stereocilium organization / retina homeostasis / hydrogen peroxide biosynthetic process / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / superoxide dismutase activity / regulation of multicellular organism growth / transmission of nerve impulse / response to axon injury / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / removal of superoxide radicals / sensory perception of sound / dendrite cytoplasm / regulation of mitochondrial membrane potential / positive regulation of cytokine production / glutathione metabolic process / locomotory behavior / response to hydrogen peroxide / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / proteasome-mediated ubiquitin-dependent protein catabolic process / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm
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
AZIDE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFerraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / Wilson, K.S. / Mangani, S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1998
Title: Crystallographic determination of reduced bovine superoxide dismutase at pH 5.0 and of anion binding to its active site
Authors: Ferraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / Mangani, S.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CU-ZN SUPEROXIDE DISMUTASE)
B: PROTEIN (CU-ZN SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56910
Polymers31,1472
Non-polymers4228
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.600, 197.500, 50.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (CU-ZN SUPEROXIDE DISMUTASE) / SOD


Mass: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P00442, superoxide dismutase

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Non-polymers , 5 types, 352 molecules

#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.5 Å3/Da / Density % sol: 73 %
Crystal growMethod: excess nitrogen atmosphere / pH: 5
Details: 20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: free interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG600011
250 mM11NaN3
37 mg/mlprotein12

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 213345 / % possible obs: 87.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 8.07 / % possible all: 85.5
Reflection
*PLUS
Num. obs: 30955 / Num. measured all: 213345
Reflection shell
*PLUS
% possible obs: 85.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SXC

1sxc


Resolution: 2.05→10 Å / σ(F): 0
Details: SIMILAR TO STRUCTURES 1SXA, 1SXB, 1SXC AND 1SXN, GLU 119 IN BOTH SUBUNITS APPEAR TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND THE ELECTRON DENSITY OCCURRING CLOSE ...Details: SIMILAR TO STRUCTURES 1SXA, 1SXB, 1SXC AND 1SXN, GLU 119 IN BOTH SUBUNITS APPEAR TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND THE ELECTRON DENSITY OCCURRING CLOSE TO ITS SIDE CHAIN HAS BEEN TENTATIVELY MODELED AS CALCIUM IONS WITH 0.5 OCCUPANCY (IUM 154 A AND IUM 154 B). SEE PDB ENTRY 1SXC.
RfactorNum. reflection% reflection
Rwork0.166 --
all-30955 -
obs-30955 87.8 %
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 12 344 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3963
X-RAY DIFFRACTIONp_mcangle_it3.6454
X-RAY DIFFRACTIONp_scbond_it4.7284.5
X-RAY DIFFRACTIONp_scangle_it7.0266
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1820.15
X-RAY DIFFRACTIONp_singtor_nbd0.1930.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2090.3
X-RAY DIFFRACTIONp_planar_tor1.812.5
X-RAY DIFFRACTIONp_staggered_tor12.35710
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.7725
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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