[English] 日本語
Yorodumi
- PDB-1bzo: THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bzo
TitleTHREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.
ComponentsPROTEIN (SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / MONOMERIC CU / ZN SUPEROXIDE DISMUTASE / PROTEIN-SUBUNIT RECOGNITION / PROTEIN ELECTROSTATIC
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding
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 / URANYL (VI) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesPhotobacterium leiognathi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBordo, D. / Matak, D. / Djinovic-Carugo, K. / Rosano, C. / Pesce, A. / Bolognesi, M. / Stroppolo, M.E. / Falconi, M. / Battistoni, A. / Desideri, A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.
Authors: Bordo, D. / Matak, D. / Djinovic-Carugo, K. / Rosano, C. / Pesce, A. / Bolognesi, M. / Stroppolo, M.E. / Falconi, M. / Battistoni, A. / Desideri, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Novel Dimeric Interface and Electrostatic Recognition in Bacterial Cu,Zn Superoxide Dismutase
Authors: Bourne, Y. / Redford, S.M. / Steinman, H.M. / Lepock, J.R. / Tainer, J.A. / Getzoff, E.D.
History
DepositionNov 2, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 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: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4835
Polymers15,8141
Non-polymers6694
Water1,838102
1
A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,96610
Polymers31,6282
Non-polymers1,3388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)86.890, 86.890, 99.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein PROTEIN (SUPEROXIDE DISMUTASE)


Mass: 15813.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Cellular location: PERIPLASMIC SPACE / Production host: Escherichia coli (E. coli) / References: UniProt: P00446, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2U
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsACTIVE SITE CATALYTIC ION COORDINATED TO HIS44, HIS46, HIS61 AND HIS118 ACTIVE SITE METAL ION ...ACTIVE SITE CATALYTIC ION COORDINATED TO HIS44, HIS46, HIS61 AND HIS118 ACTIVE SITE METAL ION COORDINATED TO HIS61, HIS69, HIS78 AND ASP81 URANYL ATOMS USED TO SOLVE A PREVIOUS STRUCTURE IN C2 SPACE GROUP (DATA NOT SUBMITTED)
Sequence detailsTHE PROTEIN USED IS A TRUNCATED FORM, WITHOUT THE FIRST 22 RESIDUES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 45.88 %
Crystal growpH: 4
Details: PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, T=28C
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 28 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
3100 mMsodium chloride1reservoir
450 mMsodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→24.7 Å / Num. obs: 8469 / % possible obs: 96 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.09

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUS MODEL OF THE PROTEIN IN SPACE GROUP C2 NOT DEPOSITED IN PDB

Resolution: 2.1→24.7 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
all8469 -
obs8075 96 %
Solvent computationBsol: 206 Å2 / ksol: 0.77 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 4 102 1215
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01811375.5
X-RAY DIFFRACTIONt_angle_deg2.6215339.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017275.5
X-RAY DIFFRACTIONt_gen_planes0.01816925.5
X-RAY DIFFRACTIONt_it4.25113715
X-RAY DIFFRACTIONt_nbd0.0672021
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_planar_d / Dev ideal: 0.01

+
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