[English] 日本語
Yorodumi
- PDB-3ot7: Escherichia coli apo-manganese superoxide dismutase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ot7
TitleEscherichia coli apo-manganese superoxide dismutase
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE / superoxide dismutase / manganese enzyme / metalloprotein / DNA binding
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 / cytosol / 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 / 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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / 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: 1.901 Å
AuthorsWhittaker, M.M. / Lerch, T.F. / Kirillova, O. / Chapman, M.S. / Whittaker, J.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2011
Title: Subunit dissociation and metal binding by Escherichia coli apo-manganese superoxide dismutase.
Authors: Whittaker, M.M. / Lerch, T.F. / Kirillova, O. / Chapman, M.S. / Whittaker, J.W.
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
C: Superoxide dismutase [Mn]
D: Superoxide dismutase [Mn]


Theoretical massNumber of molelcules
Total (without water)91,9884
Polymers91,9884
Non-polymers00
Water11,530640
1
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]


Theoretical massNumber of molelcules
Total (without water)45,9942
Polymers45,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area17130 Å2
MethodPISA
2
C: Superoxide dismutase [Mn]
D: Superoxide dismutase [Mn]


Theoretical massNumber of molelcules
Total (without water)45,9942
Polymers45,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.875, 106.548, 178.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-634-

HOH

31C-265-

HOH

DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

-
Components

#1: Protein
Superoxide dismutase [Mn] / MnSOD


Mass: 22996.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: sodA, b3908, JW3879 / Plasmid: pBAS2sodA / Production host: Escherichia coli (E. coli) / Strain (production host): BW25113 delta sodA / References: UniProt: P00448, superoxide dismutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 6000, 0.1M Bicine, 1mM EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44 Å / Num. obs: 70968 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Χ2: 1.482 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.935.40.54635082.20699.4
1.93-1.975.90.42534870.8299.5
1.97-2.016.40.39934740.73799.8
2.01-2.056.90.38635500.767100
2.05-2.097.20.38335011.885100
2.09-2.147.40.27335160.839100
2.14-2.197.50.2335180.861100
2.19-2.257.50.26735252.33100
2.25-2.327.50.19535261.169100
2.32-2.397.50.15335220.979100
2.39-2.487.50.14435300.973100
2.48-2.587.50.1235261.044100
2.58-2.77.50.10935541.28100
2.7-2.847.50.08335501.205100
2.84-3.027.50.07235401.395100
3.02-3.257.50.05935981.608100
3.25-3.587.50.05235691.939100
3.58-4.097.50.04935832.721100
4.09-5.157.40.04336192.402100
5.15-447.20.0437722.30999.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VEW

1vew


Resolution: 1.901→39.643 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.28 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 3569 5.05 %
Rwork0.1917 --
obs0.194 70694 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.554 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 159.48 Å2 / Biso mean: 47.4839 Å2 / Biso min: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.1368 Å20 Å2-0 Å2
2--1.3796 Å2-0 Å2
3----12.5163 Å2
Refinement stepCycle: LAST / Resolution: 1.901→39.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 0 640 7152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066741
X-RAY DIFFRACTIONf_angle_d1.0339152
X-RAY DIFFRACTIONf_chiral_restr0.075956
X-RAY DIFFRACTIONf_plane_restr0.0041191
X-RAY DIFFRACTIONf_dihedral_angle_d16.192386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9009-1.92690.31651340.28962571270596
1.9269-1.95450.28681360.2462608274499
1.9545-1.98360.30941520.24252699285199
1.9836-2.01460.30461310.243626492780100
2.0146-2.04770.3211290.2526872816100
2.0477-2.0830.28551360.251826722808100
2.083-2.12080.28931250.246126712796100
2.1208-2.16160.33011400.245827142854100
2.1616-2.20580.3031500.239226292779100
2.2058-2.25370.33251490.24412659280899
2.2537-2.30610.3211540.23826782832100
2.3061-2.36380.29751350.228626902825100
2.3638-2.42770.29111410.233326502791100
2.4277-2.49910.29441210.227627012822100
2.4991-2.57980.24481340.2326822816100
2.5798-2.6720.32971530.23732663281699
2.672-2.77890.27911420.22122700284299
2.7789-2.90540.24691650.22162647281299
2.9054-3.05850.27491470.20492688283599
3.0585-3.250.23481600.195827042864100
3.25-3.50080.2351540.184826712825100
3.5008-3.85280.20161340.15192716285099
3.8528-4.40970.16241420.131427482890100
4.4097-5.55340.17881490.128927652914100
5.5534-39.6520.14671560.143728633019100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1927-0.9899-0.48763.37012.66824.1539-0.1852-0.15310.1743-0.20220.4559-0.35990.65990.5629-0.18960.23060.18080.04590.1922-0.0570.191841.366814.551210.9744
21.2718-0.3694-0.59462.1691.92433.19790.0477-0.09120.0451-0.3119-0.47250.1736-0.259-0.82390.38070.08770.1204-0.05460.3081-0.12180.167917.395628.329420.6641
30.6556-0.0097-0.42361.03161.30353.4508-0.1029-0.1835-0.04090.03480.2534-0.02640.22190.6285-0.15560.13370.0301-0.00680.3056-0.00670.190780.24669.884433.0826
41.4965-0.3256-1.36180.6861.02823.3160.39250.00640.1442-0.6949-0.04130.0322-1.6805-0.1106-0.32350.91620.00370.06560.15730.03030.221870.232936.0824.0414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA1 - 205
2X-RAY DIFFRACTION2Chain BB1 - 205
3X-RAY DIFFRACTION3Chain CC1 - 205
4X-RAY DIFFRACTION4Chain DD1 - 205

+
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