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- PDB-1sxs: Reduced bovine superoxide dismutase at pH 5.0 complexed with thio... -

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Basic information

Entry
Database: PDB / ID: 1sxs
TitleReduced bovine superoxide dismutase at pH 5.0 complexed with thiocyanate
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 / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / superoxide dismutase activity / transmission of nerve impulse / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of cytokine production / regulation of mitochondrial membrane potential / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytoplasm / 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 / THIOCYANATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFerraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / 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 24, 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_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_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_conn.ptnr2_symmetry / _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)31,60110
Polymers31,1472
Non-polymers4548
Water6,215345
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) / CU-ZN 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, 353 molecules

#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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, 100MM NASCN, 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
2100 mM11NaSCN
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: Oct 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→10 Å / Num. obs: 200034 / % possible obs: 96.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.6 / % possible all: 90.7
Reflection
*PLUS
Num. obs: 34111 / Num. measured all: 200034
Reflection shell
*PLUS
% possible obs: 90.7 %

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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→10 Å / σ(F): 0
Details: SIMILAR TO STRUCTURES 1SXA, 1SXB AND 1SXC, GLU 119 IN BOTH SUBUNITS APPEAR TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND THE ELECTRON DENSITY OCCURRING CLOSE TO ...Details: SIMILAR TO STRUCTURES 1SXA, 1SXB AND 1SXC, 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 (CA 154 A AND CA 154 B). SEE PDB ENTRY 1SXC.
RfactorNum. reflection% reflection
Rwork0.175 --
all-34111 -
obs-34111 96.9 %
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 12 345 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7393
X-RAY DIFFRACTIONp_mcangle_it3.2814
X-RAY DIFFRACTIONp_scbond_it4.4424.5
X-RAY DIFFRACTIONp_scangle_it6.9376
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1790.15
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.7032.5
X-RAY DIFFRACTIONp_staggered_tor13.62410
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.6225
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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