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- PDB-2xjk: Monomeric Human Cu,Zn Superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 2xjk
TitleMonomeric Human Cu,Zn Superoxide dismutase
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / METAL-BINDING / PROTEIN FOLDING / NEURODEGENERATION
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.4Dec 20, 2023Group: 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_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_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.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
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)16,1436
Polymers15,8171
Non-polymers3255
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.160, 49.480, 80.440
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: 15817.432 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
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 7 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 51 TO GLU ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, CYS 7 TO ALA 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

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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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growpH: 6 / Details: 25% PEG 6000, 0.1M MES (PH 6.0), 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: Dec 13, 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: 1.45→40 Å / Num. obs: 25245 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFM

1mfm


Resolution: 1.45→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.574 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.069 / 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
Rfree0.19944 1282 5.1 %RANDOM
Rwork0.16615 ---
obs0.16788 23963 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2--0.73 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 5 153 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211149
X-RAY DIFFRACTIONr_bond_other_d0.0010.02758
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9491551
X-RAY DIFFRACTIONr_angle_other_deg0.84231882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35926.07851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07315198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
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_it1.2171.5750
X-RAY DIFFRACTIONr_mcbond_other0.2931.5324
X-RAY DIFFRACTIONr_mcangle_it2.07821201
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3843399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7434.5350
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.06631907
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 97 -
Rwork0.267 1753 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: -12.8784 Å / Origin y: -3.4637 Å / Origin z: 10.1639 Å
111213212223313233
T0.0041 Å20.0046 Å2-0.0028 Å2-0.008 Å2-0.0047 Å2--0.0055 Å2
L0.5905 °2-0.0516 °2-0.4128 °2-0.5753 °20.2605 °2--0.727 °2
S-0.0207 Å °-0.0276 Å °0.0301 Å °0.0374 Å °0.0263 Å °0.0034 Å °0.0229 Å °0.0319 Å °-0.0056 Å °

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