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- PDB-2v0a: Atomic resolution crystal structure of Human Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 2v0a
TitleAtomic resolution crystal structure of Human Superoxide Dismutase
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / DISEASE MUTATION / MOLECULAR DINAMICS / AMYOTROPHIC LATERAL SCLEROSIS / ZN SUPEROXIDE DISMUTASE / METAL-BINDING / OXIOREDUCTASE / ZINC / COPPER / HUMAN CU / ACETYLATION / ANTIOXIDANT
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein 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
ACETATE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.15 Å
AuthorsStrange, R.W. / Antonyuk, S. / Yong, C.W. / Smith, W. / Hasnain, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Molecular Dynamics Using Atomic-Resolution Structure Reveal Structural Fluctuations that May Lead to Polymerization of Human Cu-Zn Superoxide Dismutase.
Authors: Strange, R.W. / Yong, C.W. / Smith, W. / Hasnain, S.S.
History
DepositionMay 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,26010
Polymers31,6552
Non-polymers6058
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.545, 68.220, 50.306
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein SUPEROXIDE DISMUTASE


Mass: 15827.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HUMAN BLOOD / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 584 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2 Å3/Da / Density % sol: 38 %
Crystal growpH: 4.75
Details: 3.5 M AMMONIUM SULPHATE, 100MM NACL, 50MM ACETATE BUFFER PH 4.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→21.5 Å / Num. obs: 88555 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.15→21.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.746 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3458 4 %RANDOM
Rwork0.155 ---
obs0.157 88555 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0.56 Å2
2---1.43 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.15→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 23 576 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212436
X-RAY DIFFRACTIONr_bond_other_d0.0020.022141
X-RAY DIFFRACTIONr_angle_refined_deg2.2091.9593291
X-RAY DIFFRACTIONr_angle_other_deg2.58335064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8125321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08525.872109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2115415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.232159
X-RAY DIFFRACTIONr_chiral_restr0.1550.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022775
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02432
X-RAY DIFFRACTIONr_nbd_refined0.3690.2632
X-RAY DIFFRACTIONr_nbd_other0.2590.22388
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21157
X-RAY DIFFRACTIONr_nbtor_other0.1040.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.280.2413
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.22721616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.11442509
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.446904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7518779
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 259
Rwork0.279 5594

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