[English] 日本語
Yorodumi
- PDB-1yai: X-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yai
TitleX-RAY STRUCTURE OF A BACTERIAL COPPER,ZINC SUPEROXIDE DISMUTASE
ComponentsCOPPER, ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / BETA-BARREL / METALLOENZYME / MACROMOLECULAR ASSEMBLY
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 / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesPhotobacterium leiognathi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBourne, Y. / Redford, S.M. / Lo, T.P. / Tainer, J.A. / Getzoff, E.D.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallographic Characterization of a Cu,Zn Superoxide Dismutase from Photobacterium Leiognathi
Authors: Redford, S.M. / Mcree, D.E. / Getzoff, E.D. / Steinman, H.M. / Tainer, J.A.
History
DepositionFeb 3, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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_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
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: COPPER, ZINC SUPEROXIDE DISMUTASE
B: COPPER, ZINC SUPEROXIDE DISMUTASE
C: COPPER, ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7929
Polymers47,4053
Non-polymers3876
Water6,449358
1
A: COPPER, ZINC SUPEROXIDE DISMUTASE
hetero molecules

A: COPPER, ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8626
Polymers31,6042
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
B: COPPER, ZINC SUPEROXIDE DISMUTASE
C: COPPER, ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8626
Polymers31,6042
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.700, 87.000, 43.500
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.20969, -0.65398, -0.72687), (-0.62691, -0.48056, 0.61323), (-0.75034, 0.58427, -0.30922)
Vector: 82.8228, 75.59549, 23.09389)

-
Components

#1: Protein COPPER, ZINC SUPEROXIDE DISMUTASE / CU / ZN SUPEROXIDE DISMUTASE / CU / ZN SOD


Mass: 15801.800 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Strain: MC1061 / Gene: PHSOD / Plasmid: PPHSOD1LACI / Gene (production host): PHSOD / Production host: Escherichia coli (E. coli) / References: UniProt: P00446, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN ALL THREE CHAINS, ARG 144 IS THE CATALYTICALLY IMPORTANT RESIDUE FOR SUPEROXIDE ANION ...IN ALL THREE CHAINS, ARG 144 IS THE CATALYTICALLY IMPORTANT RESIDUE FOR SUPEROXIDE ANION RECOGNITION. LYS 57, ASP 58 AND LYS 60 IN SS LOOP MAY HAVE A ROLE IN THE LONG-RANGE ATTRACTION OF THE FREE RADICAL ANION. THE DIMER INTERFACE IS COMPLETED BY AN UNUSUAL RING OF 11 HYDROGEN-BONDED SOLVENT MOLECULES BURIED WITHIN A CAVITY FILLING THE DIMER INTERFACE BETWEEN TWO HYDROPHOBIC CLUSTERS.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5 / Details: 42% MPD, 60 MM POTASSIUM PHOSPHATE, PH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
260 mMpotassium phosphate1drop
342 %MPD1reservoir
460 mMpotassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 20, 1991
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 116490 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.049
Reflection
*PLUS
Num. obs: 30277 / Num. measured all: 116490 / Rmerge(I) obs: 0.049

-
Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SOD

3sod


Resolution: 1.9→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: X-PLOR ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1371 5 %EVERY 20TH REFLECTION
Rwork0.149 ---
all-28333 --
obs-26942 75 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 204 Å2 / ksol: 0.65 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 6 358 3678
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01333950.8
X-RAY DIFFRACTIONt_angle_deg2.32645761.3
X-RAY DIFFRACTIONt_dihedral_angle_d17.80220220
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014821.2
X-RAY DIFFRACTIONt_gen_planes0.0155063.8
X-RAY DIFFRACTIONt_it3.43733951.3
X-RAY DIFFRACTIONt_nbd0.0272115
Software
*PLUS
Name: TNT / Version: 5EB / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.8020
X-RAY DIFFRACTIONt_plane_restr0.015

+
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