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- PDB-3hw7: High pressure (0.57 GPa) crystal structure of bovine copper, zinc... -

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Basic information

Entry
Database: PDB / ID: 3hw7
TitleHigh pressure (0.57 GPa) crystal structure of bovine copper, zinc superoxide dismutase at 2.0 angstroms
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / METAL BINDING PROTEIN / BOVINE / SUPEROXIDE DISMUTASE / high pressure / flexible electrostatic loop / Antioxidant / Disulfide bond / Metal-binding
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / positive regulation of catalytic activity / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / positive regulation of catalytic activity / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / 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 / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / 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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / COPPER (I) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAscone, I. / Savino, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa
Authors: Ascone, I. / Savino, C. / Kahn, R. / Fourme, R.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,4687
Polymers31,1472
Non-polymers3215
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.845, 50.509, 146.377
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: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ERYTHROCYTES / References: UniProt: P00442, superoxide dismutase
#2: Chemical ChemComp-CU1 / COPPER (I) 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.331 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2005
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.331 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. obs: 22012 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2893 / % possible all: 83.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CCP4model building
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBJ

1cbj


Resolution: 2→19.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.439 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21808 1121 5.1 %RANDOM
Rwork0.17208 ---
all0.17445 26546 --
obs0.17445 20848 90.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.211 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2---0.98 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 5 206 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212222
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.953006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91425.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77215358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.551158
X-RAY DIFFRACTIONr_chiral_restr0.10.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021688
X-RAY DIFFRACTIONr_nbd_refined0.1890.21159
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2173
X-RAY DIFFRACTIONr_metal_ion_refined0.070.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.217
X-RAY DIFFRACTIONr_mcbond_it1.0841.51500
X-RAY DIFFRACTIONr_mcangle_it1.72522354
X-RAY DIFFRACTIONr_scbond_it2.9193770
X-RAY DIFFRACTIONr_scangle_it4.3154.5652
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 73 -
Rwork0.199 1464 -
obs--87.13 %

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