[English] 日本語
Yorodumi
- PDB-1ix9: Crystal Structure of the E. coli Manganase(III) superoxide dismut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ix9
TitleCrystal Structure of the E. coli Manganase(III) superoxide dismutase mutant Y174F at 0.90 angstroms resolution.
ComponentsSuperoxide Dismutase
KeywordsOXIDOREDUCTASE / MANGANESE SUPEROXIDE DISMUTASE / Y174F MUTANT / HYDROGEN BOND / REACTIVITY
Function / homology
Function and homology information


cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsAnderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
Citation
Journal: To be Published
Title: Structures at 0.90 A resolution of the oxidised and reduced forms of the Y174F mutant of the manganese superoxide dismutase from Escherichia coli
Authors: Anderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#1: Journal: Biochemistry / Year: 2001
Title: Removing a Hydrogen Bond in the Dimer Interface of Escherichia Coli Manganese Superoxide Dismutase Alters Structure and Reactivity
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#2: Journal: Biochemistry / Year: 2001
Title: Outer Sphere Mutations Perturb Metal Reactivity in Manganese Superoxide Dismutase
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
History
DepositionJun 17, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide Dismutase
B: Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0724
Polymers45,9622
Non-polymers1102
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-12 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.893, 46.017, 95.993
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Superoxide Dismutase / MnSOD


Mass: 22980.877 Da / Num. of mol.: 2 / Mutation: Y174F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PDT1-5 / Production host: Escherichia coli (E. coli) / Strain (production host): QC781 / References: UniProt: P00448, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.22 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16-20% PEG6000, 0.1M BICINE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1998
RadiationMonochromator: BENT GERMANIUM SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 0.9→30 Å / Num. all: 287367 / Num. obs: 287367 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 41.5
Reflection shellResolution: 0.9→0.91 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6474 / % possible all: 67.8

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MN-SOD FROM 1IOH

1ioh


Resolution: 0.9→30 Å / Num. parameters: 39676 / Num. restraintsaints: 44548 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent species is assigned as a hydroxide ion. However, a soft vibrational mode involving a putative second hydrogen atom could render this atom undetectable in difference Fourier maps. THE CLOSE CONTACTS AND POOR GEOMETRY LISTED IN REMARK 500 ARE CAUSED BY PARTIAL OCCUPANCIES AND DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.1274 2940 1 %RANDOM SHELL
Rwork0.1072 ---
all0.1074 287367 --
obs0.1074 287367 95.2 %-
Solvent computationSolvent model: P.C.MOEWS & R.H.KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeNum. disordered residues: 41 / Occupancy sum hydrogen: 2913.71 / Occupancy sum non hydrogen: 3982.07
Refinement stepCycle: LAST / Resolution: 0.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 6 896 4379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0144
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.088
LS refinement shellResolution: 0.9→0.91 Å
RfactorNum. reflection% reflection
Rwork0.275 --
obs-6472 67.22 %

+
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