[English] 日本語
Yorodumi
- PDB-2sod: DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sod
TitleDETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE
ComponentsCOPPER,ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / 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 / dendrite cytoplasm / embryo implantation / glutathione metabolic process / 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 / negative regulation of neuron apoptotic process / response to ethanol / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / 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 (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
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.
Authors: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C.
#1: Journal: Nature / Year: 1983
Title: Structure and Mechanism of Copper, Zinc Superoxide Dismutase
Authors: Tainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C.
#2: Journal: Nature / Year: 1983
Title: Electrostatic Recognition between Superoxide and Copper, Zinc Superoxide Dismutase
Authors: Getzoff, E.D. / Tainer, J.A. / Weiner, P.K. / Kollman, P.A. / Richardson, J.S. / Richardson, D.C.
#3: Journal: Biochemistry / Year: 1977
Title: Metal Sites of Copper-Zinc Superoxide Dismutase
Authors: Beem, K.M. / Richardson, D.C. / Rajagopalan, K.V.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: Similarity of Three-Dimensional Structure between the Immunoglobulin Domain and the Copper,Zinc Superoxide Dismutase Subunit
Authors: Richardson, J.S. / Richardson, D.C. / Thomas, K.A. / Silverton, E.W. / Davies, D.R.
#5: Journal: Biochem.Biophys.Res.Commun. / Year: 1975
Title: Alpha-Carbon Coordinates for Bovine Cu,Zn Superoxide Dismutase
Authors: Richardson, J.S. / Thomas, R.A. / Richardson, D.C.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Crystal Structure of Bovine Cu,Zn Superoxide Dismutase at 3 Angstroms Resolution,Chain Tracing and Metal Ligands
Authors: Richardson, J.S. / Thomas, K.A. / Rubin, B.H. / Richardson, D.C.
#7: Journal: J.Biol.Chem. / Year: 1974
Title: The Crystal Structure of Bovine Cu2+,Zn2+ Superoxide Dismutase at 5.5 Angstroms Resolution
Authors: Thomas, K.A. / Rubin, B.H. / Bier, C.J. / Richardson, J.S. / Richardson, D.C.
#8: Journal: J.Biol.Chem. / Year: 1972
Title: Two Crystal Forms of Bovine Superoxide Dismutase
Authors: Richardson, D.C. / Bier, C.J. / Richardson, J.S.
History
DepositionMar 25, 1980Processing site: BNL
SupersessionMay 7, 1980ID: 1SOD
Revision 1.0May 7, 1980Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_database_status / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _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_asym_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_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION ...SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A WATER MOLECULE. THE DOMINANT STRUCTURAL FEATURE OF EACH MONOMER IS AN EIGHT-STRANDED ANTI-PARALLEL BETA-BARREL. THERE ARE, HOWEVER, NO HYDROGEN BONDS BETWEEN STRANDS 4 AND 5. THIS BARREL IS DESCRIBED IN SHEET RECORDS BELOW AS A NINE-STRANDED SHEET WITH IDENTICAL FIRST AND LAST STRANDS.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: COPPER,ZINC SUPEROXIDE DISMUTASE
Y: COPPER,ZINC SUPEROXIDE DISMUTASE
B: COPPER,ZINC SUPEROXIDE DISMUTASE
G: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,91312
Polymers62,3984
Non-polymers5168
Water724
1
O: COPPER,ZINC SUPEROXIDE DISMUTASE
Y: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4576
Polymers31,1992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COPPER,ZINC SUPEROXIDE DISMUTASE
G: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4576
Polymers31,1992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-36 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.650, 90.330, 71.650
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.78114, 0.20408, -0.59006), (0.16219, -0.8463, -0.50742), (-0.60292, -0.49207, 0.62798)-59.69421, 29.26225, -12.96087
2given(-0.76664, -0.06756, 0.63852), (0.20331, 0.91774, 0.34121), (-0.60904, 0.3914, -0.68983)-53.22701, -0.63586, -21.95514
3given(0.99226, -0.0164, -0.12309), (0.00386, -0.98668, 0.16263), (-0.12412, -0.16185, -0.97898)-2.98838, 32.25722, 3.3424
DetailsTHE TRANSFORMATION WHICH WILL PLACE THE YELLOW MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 1 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE BLUE MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 2 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE GREEN MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 3 BELOW.

-
Components

#1: Protein
COPPER,ZINC SUPEROXIDE DISMUTASE


Mass: 15599.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00442, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / 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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mg/mlenzyme 1drop
20.5 Mphosphate1reservoir
358 %(v/v)MPD1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 4 Å / Num. obs: 17206 / % possible obs: 35 %

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.256 / Highest resolution: 2 Å
Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER ...Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER COMPRISES MONOMERS BLUE (B) AND GREEN (G). ONLY THOSE HYDROGEN BONDS OF WHICH THE DEPOSITORS ARE MOST CERTAIN ARE PRESENTED ON THE CONECT RECORDS BELOW.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 8 4 4392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.039
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 4 Å / Highest resolution: 2 Å / Rfactor obs: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12 Å2
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.03
LS refinement shell
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more