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- PDB-1sxc: CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUT... -

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Basic information

Entry
Database: PDB / ID: 1sxc
TitleCRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE ACCEPTOR
Function / homology
Function and homology information


neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / glutathione metabolic process / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / regulation of mitochondrial membrane potential / locomotory behavior / response to organic substance / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / 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, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsRypniewski, W.R. / Mangani, S. / Bruni, B. / Orioli, P. / Casati, M. / Wilson, K.S.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of reduced bovine erythrocyte superoxide dismutase at 1.9 A resolution.
Authors: Rypniewski, W.R. / Mangani, S. / Bruni, B. / Orioli, P.L. / Casati, M. / Wilson, K.S.
History
DepositionMar 17, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4056
Polymers31,1472
Non-polymers2584
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-36 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.800, 51.060, 147.990
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: (-0.59865, -0.79544, 0.09433), (-0.79182, 0.56987, -0.21973), (0.12102, -0.20623, -0.97099)
Vector: 23.94056, 28.30711, 119.76434)
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 1 .. A 151 B 1 .. B 151 0.295

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Components

#1: Protein SUPEROXIDE DISMUTASE /


Mass: 15573.337 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00442, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


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 / Water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND REDUCED WITH SODIUM DITHIONITE TO CU(I).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.56 %
Description: THIS IS THE FINAL MODEL OBTAINED AFTER COMBINING TWO COMPLETE DATA SETS, COLLECTED FROM TWO DIFFERENT CRYSTALS. TWO OTHER MODELS OBTAINED BY REFINING AGAINST THE INDIVIDUAL DATA SETS ...Description: THIS IS THE FINAL MODEL OBTAINED AFTER COMBINING TWO COMPLETE DATA SETS, COLLECTED FROM TWO DIFFERENT CRYSTALS. TWO OTHER MODELS OBTAINED BY REFINING AGAINST THE INDIVIDUAL DATA SETS WERE USED TO ESTIMATE ATOMIC COORDINATE ERRORS FOR THIS FINAL MODEL. THIS MODEL AND THE CORRESPONDING STRUCTURE FACTORS ARE OF UNUSUALLY HIGH QUALITY FOR THIS RESOLUTION (1.9 ANGSTROMS), WITH 97% COMPLETENESS, 9.1 FOLD REDUNDANCY (TWO DATA SETS COMBINED) AND HIGH QUALITY X-RAY SOURCE (SYNCHROTRON). THE COORDINATE ERROR IN THE FINAL MODEL, ESTIMATED FROM COMPARING THE TWO INDEPENDENTLY REFINED MODELS WAS 0.08 ANGSTROMS FOR PROTEIN ATOMS, 0.07 ANGSTROMS FOR MAIN CHAIN, 0.09 ANGSTROMS FOR SIDE CHAINS. THE OTHER TWO MODELS AND THE CORRESPONDING DATA SETS HAVE BEEN DEPOSITED SEPARATELY.
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
316 %(w/v)PEG600012
2Tris-HCl11
4Tris-HCl12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.97 Å
DetectorType: CUSTOM-MADE / Detector: IMAGE PLATE / Date: Nov 16, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionNum. obs: 28249 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Rmerge(I) obs: 0.01

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Processing

Software
NameClassification
DENZOdata reduction
PROLSQrefinement
RefinementResolution: 1.9→10 Å / σ(F): 0
Details: GLU 119 (BOTH SUBUNITS) APPEARS ON THE ELECTRON DENSITY TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND IT HAS NOT BEEN MODELLED. THE APPEARANCE OF THE ELECTRON ...Details: GLU 119 (BOTH SUBUNITS) APPEARS ON THE ELECTRON DENSITY TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND IT HAS NOT BEEN MODELLED. THE APPEARANCE OF THE ELECTRON DENSITY IS CONSISTENT WITH OE1 REPLACED BY A HYDROXYLAMINE GROUP. THE MODIFICATION IS ALSO OBSERVED IN THE STRUCTURE OF NATIVE, OXIDIZED SOD. THEREFORE, IT CANNOT BE AN ARTIFACT OF THE TREATMENT WITH DITHIONITE, USED IN REDUCING THE ENZYME. THE POSITION OF THE MODIFICATION RELATIVE TO THE ACTIVE SITE SUGGESTS A ROLE IN THE REACTION MECHANISM. SEE THE PAPER CITED ON JRNL RECORDS ABOVE FOR DETAILS. RESIDUES WITH POOR ELECTRON DENSITY: LYS A 3, LYS A 9, LYS A 23, LYS A 68, LYS A 73, LYS A 89, GLU A 107, LYS A 120, LYS A 134, LYS A 151, LYS B 23, ASN B 51, GLN B 53, LYS B 73, LYS B 89, LYS B 134, LYS B 151. A NUMBER OF CLOSE CONTACTS OCCURS BETWEEN SOLVENT MOLECULES. INSPECTION OF THE ELECTRON DENSITY CONFIRMS THAT THESE SITES ARE REAL BUT PROBABLY CORRESPOND TO PARTIALLY OCCUPIED, ALTERNATIVE SOLVENT SITES. A FEW VERY CLOSE CONTACTS OCCUR BETWEEN ATOMS WITH ZERO OCCUPANCY AND SOLVENT MOLECULES.
RfactorNum. reflection% reflection
obs0.156 28249 97 %
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 4 367 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.33
X-RAY DIFFRACTIONp_mcangle_it3.14
X-RAY DIFFRACTIONp_scbond_it4.84.5
X-RAY DIFFRACTIONp_scangle_it76
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1840.2
X-RAY DIFFRACTIONp_singtor_nbd0.1920.5
X-RAY DIFFRACTIONp_multtor_nbd0.3540.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2530.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.75
X-RAY DIFFRACTIONp_staggered_tor13.215
X-RAY DIFFRACTIONp_orthonormal_tor37.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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