[English] 日本語
Yorodumi
- PDB-1wb7: Iron Superoxide Dismutase (Fe-SOD) From The Hyperthermophile Sulf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wb7
TitleIron Superoxide Dismutase (Fe-SOD) From The Hyperthermophile Sulfolobus Solfataricus. Crystal Structure of the Y41F mutant.
ComponentsSUPEROXIDE DISMUTASE [FE]
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / SOD / IRON / SUPEROXIDE RADICAL DISPROPORTIONATION / SULFOLOBUS SOLFTARICUS / THERMOSTABLE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
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 ...: / 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 [Fe]
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsGogliettino, M.A. / Tanfani, F. / Scire, A. / Ursby, T. / Adinolfi, B.S. / Cacciamani, T. / De Vendittis, E.
Citation
Journal: Biochemistry / Year: 2004
Title: The Role of Tyr41 and His155 in the Functional Properties of Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus
Authors: Gogliettino, M.A. / Tanfani, F. / Scire, A. / Ursby, T. / Adinolfi, B.S. / Cacciamani, T. / De Vendittis, E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Iron Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus: Analysis of Structure and Thermostability
Authors: Ursby, T. / Adinolfi, B.S. / Al-Karadaghi, S. / De Vendittis, E. / Bocchini, V.
#2: Journal: Eur.J.Biochem. / Year: 2001
Title: Phenylmethanesulfonyl Fluoride Inactivates an Archaeal Superoxide Dismutase by Chemical Modification of a Specific Tyrosine Residue
Authors: De Vendittis, E. / Ursby, T. / Rullo, R. / Gogliettino, M.A. / Masullo, M. / Bocchini, V.
History
DepositionOct 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2004Provider: 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 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 13, 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_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.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.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_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: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3644
Polymers48,2532
Non-polymers1122
Water4,035224
1
A: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules

A: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7298
Polymers96,5054
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)75.188, 121.753, 59.420
Angle α, β, γ (deg.)90.00, 128.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

21B-2085-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.90759, -0.000509, 0.419858), (-0.000775, -1, 0.000463), (0.419858, -0.000745, -0.90759)
Vector: -11.423, 98.119, 52.096)

-
Components

#1: Protein SUPEROXIDE DISMUTASE [FE]


Mass: 24126.312 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P80857, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE CHAIN A,B TYR 41 PHE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN HANGING DROPS AT 21C IN A 1 TO 1 MIX OF THE RESERVOIR SOLUTION (8% PEG 8000, 0.1 M TRIS/HCL PH 8.5) AND A PROTEIN SOLUTION (1.45 MG/ML Y41F-SSSOD, ...Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN HANGING DROPS AT 21C IN A 1 TO 1 MIX OF THE RESERVOIR SOLUTION (8% PEG 8000, 0.1 M TRIS/HCL PH 8.5) AND A PROTEIN SOLUTION (1.45 MG/ML Y41F-SSSOD, 20 MM TRIS/HCL PH 7.8, 1% GLYCEROL).
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 %PEG80001reservoir
20.1 MTris-HCl1reservoirpH8.5
31.45 mg/mlprotein1drop
420 mMTris-HCl1droppH7.8
51 %glycerol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.986
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 1998 / Details: PT-COATED MIRROR AND SI MONOCHROMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 2.24→60.9 Å / Num. obs: 19994 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6
Reflection shellResolution: 2.24→2.39 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 60.9 Å / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SSS

1sss
PDB Unreleased entry


Resolution: 2.24→29.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1649340.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 7 RESIDUES, ...Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 7 RESIDUES, THE IRON ION AND 48 WATER MOLECULES AND THE CORRESPONDING NCS RELEATED ATOMS. THE RMS DEVIATION FOR THE ATOMS USED FOR NCS IN THE REFINEMENT IS 0.005 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1023 5.1 %RANDOM
Rwork0.181 ---
obs0.181 19994 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5933 Å2 / ksol: 0.380503 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å22.61 Å2
2---0.16 Å20 Å2
3----0.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.24→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 2 224 3566
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.30.5
X-RAY DIFFRACTIONc_mcangle_it0.541
X-RAY DIFFRACTIONc_scbond_it2.443
X-RAY DIFFRACTIONc_scangle_it3.273.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 176 5.3 %
Rwork0.212 3153 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.222 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.754

+
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