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- PDB-2xjl: Monomeric Human Cu,Zn Superoxide dismutase without Cu ligands -

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Basic information

Entry
Database: PDB / ID: 2xjl
TitleMonomeric Human Cu,Zn Superoxide dismutase without Cu ligands
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / CU/ZN SOD1 / METAL-BINDING / NEURODEGENERATION
Function / homology
Function and homology information


positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / regulation of T cell differentiation in thymus / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide ...positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / regulation of T cell differentiation in thymus / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / regulation of GTPase activity / auditory receptor cell stereocilium organization / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / myeloid cell homeostasis / superoxide anion generation / muscle cell cellular homeostasis / superoxide metabolic process / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / heart contraction / superoxide dismutase activity / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / neuronal action potential / embryo implantation / positive regulation of superoxide anion generation / axon cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / placenta development / positive regulation of phagocytosis / dendrite cytoplasm / response to amphetamine / determination of adult lifespan / positive regulation of cytokine production / regulation of mitochondrial membrane potential / glutathione metabolic process / response to hydrogen peroxide / sensory perception of sound / locomotory behavior / response to nutrient levels / negative regulation of inflammatory response / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / gene expression / cytoplasmic vesicle / spermatogenesis / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / response to ethanol / positive regulation of MAPK cascade / lysosome / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / 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 / DI(HYDROXYETHYL)ETHER / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSaraboji, K. / Leinartaite, L. / Nordlund, A. / Oliveberg, M. / Logan, D.T.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Folding Catalysis by Transient Coordination of Zn2+ to the Cu Ligands of the Als-Associated Enzyme Cu/Zn Superoxide Dismutase 1.
Authors: Leinartaite, L. / Saraboji, K. / Nordlund, A. / Logan, D.T. / Oliveberg, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Functional Features Cause Misfolding of the Als-Provoking Enzyme Sod1.
Authors: Nordlund, A. / Leinartaite, L. / Saraboji, K. / Aisenbrey, C. / Grobner, G. / Zetterstrom, P. / Danielsson, J. / Logan, D.T. / Oliveberg, M.
History
DepositionJul 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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_alt_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1379
Polymers15,6641
Non-polymers4738
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.760, 49.220, 80.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN] / CU / ZN SUPEROXIDE DISMUTASE


Mass: 15664.223 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 153 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 7 TO ALA ENGINEERED RESIDUE IN CHAIN A, HIS 47 TO SER ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, CYS 7 TO ALA ENGINEERED RESIDUE IN CHAIN A, HIS 47 TO SER ENGINEERED RESIDUE IN CHAIN A, HIS 49 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 51 TO GLU ENGINEERED RESIDUE IN CHAIN A, GLY 52 TO GLU ENGINEERED RESIDUE IN CHAIN A, CYS 112 TO ALA ENGINEERED RESIDUE IN CHAIN A, HIS 121 TO SER
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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE
Crystal growpH: 5
Details: 25% PEG 6000, 0.1M SODIUM ACETATE (PH 5.0), 0.01M ZNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9085
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2007
RadiationMonochromator: BENT SI (220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9085 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 20574 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMERIC CU,ZN SOD1

Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.018 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS ADDED WITH U VALUES. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1055 5.1 %RANDOM
Rwork0.15551 ---
obs0.15688 19519 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.056 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2--0.97 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 17 145 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211178
X-RAY DIFFRACTIONr_bond_other_d0.0020.02781
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9641586
X-RAY DIFFRACTIONr_angle_other_deg1.94331939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59926.27551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27315202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.931155
X-RAY DIFFRACTIONr_chiral_restr0.1050.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.5776
X-RAY DIFFRACTIONr_mcbond_other0.2491.5335
X-RAY DIFFRACTIONr_mcangle_it1.67421238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4553402
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7364.5348
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.94631959
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 80 -
Rwork0.268 1397 -
obs--98.53 %
Refinement TLS params.Method: refined / Origin x: -12.4916 Å / Origin y: -3.4731 Å / Origin z: 10.1206 Å
111213212223313233
T0.0058 Å20.0018 Å20.0026 Å2-0.0051 Å2-0.0007 Å2--0.0056 Å2
L0.9008 °2-0.1415 °2-0.2992 °2-0.7031 °20.2801 °2--1.24 °2
S0.0109 Å °-0.048 Å °0.0498 Å °0.0333 Å °0.0093 Å °-0.0114 Å °0.0119 Å °0.0477 Å °-0.0202 Å °

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