[English] 日本語
Yorodumi
- PDB-1my6: The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1my6
TitleThe 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics
ComponentsIron (III) Superoxide Dismutase
KeywordsOXIDOREDUCTASE / Iron Speroxide Dismutase / thermophile / reactive oxygen species / cyanobacteria / thermosynechococcus / Thermosynechococcus elongatus / Superoxide Dismutase / SOD / FeSOD / Iron(III) Superoxide Dismutase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYoshida, S.M. / Cascio, D. / Sawaya, M.R. / Yeates, T.O. / Kerfeld, C.A.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2003
Title: The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus.
Authors: Kerfeld, C.A. / Yoshida, S. / Tran, K.T. / Yeates, T.O. / Cascio, D. / Bottin, H. / Berthomieu, C. / Sugiura, M. / Boussac, A.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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_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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron (III) Superoxide Dismutase
B: Iron (III) Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3254
Polymers44,2132
Non-polymers1122
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.749, 63.644, 74.709
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Iron (III) Superoxide Dismutase


Mass: 22106.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIR2, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111.7 mg/mlprotein1drop
210 mMTris1droppH7.5
30.1 Msodium cacodylate1reservoirpH6.7
40.2 Mmagnesium acetate tetrahydrate1reservoir
520 %PEG60001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→70 Å / Num. obs: 53851 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.18 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 6.35
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 14.28 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.35 / Num. unique all: 5643 / Rsym value: 0.32 / % possible all: 93.4
Reflection
*PLUS
% possible obs: 99.57 % / Num. measured all: 274614 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
Lowest resolution: 1.66 Å / % possible obs: 94.5 % / Rmerge(I) obs: 0.322

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FeSOD from E.coli, PDB entry 1isc

1isc


Resolution: 1.6→70 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.748 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Refined with anisotropic temperature factors. NCS restraints were not applied on the 2 molecules in the asymmetric unit.
RfactorNum. reflection% reflectionSelection details
Rfree0.23208 2896 5.1 %RANDOM
Rwork0.19377 ---
obs0.19577 53851 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.82 Å2
2---1.54 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 2 565 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213224
X-RAY DIFFRACTIONr_bond_other_d0.0020.022744
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9144396
X-RAY DIFFRACTIONr_angle_other_deg0.90336392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02686
X-RAY DIFFRACTIONr_nbd_refined0.2310.2739
X-RAY DIFFRACTIONr_nbd_other0.2470.23169
X-RAY DIFFRACTIONr_nbtor_other0.0870.21715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2387
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.51966
X-RAY DIFFRACTIONr_mcangle_it1.9123138
X-RAY DIFFRACTIONr_scbond_it2.61631258
X-RAY DIFFRACTIONr_scangle_it3.6934.51258
X-RAY DIFFRACTIONr_rigid_bond_restr1.52223224
X-RAY DIFFRACTIONr_sphericity_free3.6712567
X-RAY DIFFRACTIONr_sphericity_bonded2.12423130
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 215
Rwork0.159 4063
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2

+
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