[English] 日本語
Yorodumi
- PDB-6dtk: Heterodimers of FALS mutant SOD enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dtk
TitleHeterodimers of FALS mutant SOD enzyme
ComponentsSuperoxide dismutase C111S/D83S-C111S HETERODIMER
KeywordsOXIDOREDUCTASE / Copper/Zinc superoxide dismutase Cu / Zn-SOD1 / metal binding protein / FALS Zn-deficient SOD1
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide / regulation of GTPase activity / auditory receptor cell stereocilium organization / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / muscle cell cellular homeostasis / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / thymus development / superoxide dismutase activity / ovarian follicle development / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / transmission of nerve impulse / response to axon injury / reactive oxygen species metabolic process / placenta development / embryo implantation / positive regulation of superoxide anion generation / sensory perception of sound / response to amphetamine / axon cytoplasm / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / regulation of mitochondrial membrane potential / dendrite cytoplasm / locomotory behavior / positive regulation of cytokine production / glutathione metabolic process / response to hydrogen peroxide / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / negative regulation of neuron apoptotic process / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / positive regulation of MAPK cascade / intracellular iron ion homeostasis / lysosome / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / 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
COPPER (II) ION / MALONATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStreltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B.
CitationJournal: To Be Published
Title: Structural characterization of heterodimers of FALS mutant SOD enzyme
Authors: Streltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B.
History
DepositionJun 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase C111S/D83S-C111S HETERODIMER
C: Superoxide dismutase C111S/D83S-C111S HETERODIMER
E: Superoxide dismutase C111S/D83S-C111S HETERODIMER
G: Superoxide dismutase C111S/D83S-C111S HETERODIMER
I: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,01726
Polymers163,6265
Non-polymers1,39221
Water24,4281356
1
A: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0856
Polymers32,7251
Non-polymers3605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.699, 201.671, 143.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

-
Components

#1: Protein
Superoxide dismutase C111S/D83S-C111S HETERODIMER / Superoxide dismutase 1 / hSod1


Mass: 32725.129 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsChimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due ...Chimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due to almost two fold symmetry of the heterodimer and structural similarity to the WT protein (or possible admixture of homodimers formed due to broken linker), the crystal electron density shows an average picture with fractional mixed DS populations on positions 83 and 252.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2-3 M Ammonium sulfate or Sodium malonate / PH range: 4.5-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2013 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.57 Å / Num. obs: 158995 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.25
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.47 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUN

1fun


Resolution: 2→47.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.021 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 7971 5 %RANDOM
Rwork0.156 ---
obs0.158 150990 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--0.4 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11297 0 27 1356 12680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01511661
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710387
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.64515651
X-RAY DIFFRACTIONr_angle_other_deg1.1931.6624408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.1815.4171629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5324.494514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.406151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861539
X-RAY DIFFRACTIONr_chiral_restr0.1660.21477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022051
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_it2.833.5986289
X-RAY DIFFRACTIONr_mcbond_other2.8293.5986288
X-RAY DIFFRACTIONr_mcangle_it4.1875.3747859
X-RAY DIFFRACTIONr_mcangle_other4.1885.3747860
X-RAY DIFFRACTIONr_scbond_it3.9464.0745372
X-RAY DIFFRACTIONr_scbond_other3.9464.0745370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2435.8827791
X-RAY DIFFRACTIONr_long_range_B_refined8.99746.04112809
X-RAY DIFFRACTIONr_long_range_B_other8.81745.0112362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 576 -
Rwork0.225 10937 -
obs--98.88 %

+
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