[English] 日本語
Yorodumi
- PDB-8imd: Crystal structure of Cu/Zn Superoxide dismutase from Paenibacillu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8imd
TitleCrystal structure of Cu/Zn Superoxide dismutase from Paenibacillus lautus
ComponentsCu/Zn-Superoxide dismutase
KeywordsOXIDOREDUCTASE / Superoxide dismutase / SOD / SOD1
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesPaenibacillus lautus NBRC 15380 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsNarikiyo, S. / Furukawa, Y. / Akutsu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05765 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Characterization of a novel cysteine-less Cu/Zn-superoxide dismutase in Paenibacillus lautus missing a conserved disulfide bond.
Authors: Furukawa, Y. / Shintani, A. / Narikiyo, S. / Sue, K. / Akutsu, M. / Muraki, N.
History
DepositionMar 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cu/Zn-Superoxide dismutase
B: Cu/Zn-Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1848
Polymers46,5352
Non-polymers6486
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-20 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.240, 53.612, 169.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cu/Zn-Superoxide dismutase


Mass: 23267.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus lautus NBRC 15380 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 22.5% PEG 4,000, 100 mM acetic acid and sodium acetate buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.275 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.275 Å / Relative weight: 1
ReflectionResolution: 1.45→45.31 Å / Num. obs: 74112 / % possible obs: 99.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 15.9 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10562 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→45.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.493 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22058 3672 5 %RANDOM
Rwork0.18824 ---
obs0.18988 70347 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.45→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 28 307 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162942
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.6344433
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5826829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61725.132152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09215492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.101158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02677
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0312.3121714
X-RAY DIFFRACTIONr_mcbond_other2.0282.3131712
X-RAY DIFFRACTIONr_mcangle_it2.8013.4682160
X-RAY DIFFRACTIONr_mcangle_other2.8013.4682161
X-RAY DIFFRACTIONr_scbond_it3.1462.6361531
X-RAY DIFFRACTIONr_scbond_other3.1462.6361529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.713.8222274
X-RAY DIFFRACTIONr_long_range_B_refined5.62928.8963488
X-RAY DIFFRACTIONr_long_range_B_other5.62828.8993489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 235 -
Rwork0.318 5114 -
obs--98.67 %

+
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