[English] 日本語
Yorodumi
- PDB-1vew: MANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vew
TitleMANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI
ComponentsMANGANESE SUPEROXIDE DISMUTASE
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 / cytoplasm / cytosol
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 / 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
: / HYDROXIDE ION / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEdwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1998
Title: Crystal structure of Escherichia coli manganese superoxide dismutase at 2.1-angstrom resolution.
Authors: Edwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N.
History
DepositionJan 20, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
C: MANGANESE SUPEROXIDE DISMUTASE
D: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,27512
Polymers91,9884
Non-polymers2888
Water7,404411
1
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1386
Polymers45,9942
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area17710 Å2
MethodPISA
2
C: MANGANESE SUPEROXIDE DISMUTASE
D: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1386
Polymers45,9942
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.840, 108.910, 182.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.134086, 0.977846, 0.160742), (0.977948, 0.104362, 0.180905), (0.160122, 0.181454, -0.970276)10.109, -12.668, 22.894
2given(-0.079286, -0.99648, 0.027237), (-0.996167, 0.080214, 0.034875), (-0.036937, -0.024368, -0.99902)103.408, 51.431, 46.994
3given(-0.956616, -0.172522, -0.234782), (0.21721, -0.959375, -0.180053), (-0.194181, -0.223239, 0.955227)115.999, 41.21, 24.594

-
Components

#1: Protein
MANGANESE SUPEROXIDE DISMUTASE / MNSOD / MNSD


Mass: 22996.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: AB2463/PDT1-5 / References: UniProt: P00448, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND CONSISTED OF 2UL OF WELL SOLUTION AND 2UL OF PROTEIN SOLUTION (MNSOD AT 12MG/ML IN WATER)., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
28-15 %PEG60001drop
30.025 Mbicine titrated1drop
416-30 %PEG60001reservoir
50.05 Mbicine titrated1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: 0.3MM DIAMETER COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 56890 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 0.7 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.191 / % possible all: 77
Reflection
*PLUS
Num. measured all: 215051 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.191

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MNG

1mng


Resolution: 2.1→50 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT CSDX-PROTGEO
RfactorNum. reflection% reflection
Rfree0.21 2874 5 %
Rwork0.188 --
all0.186 53872 -
obs0.186 53872 92 %
Solvent computationSolvent model: MOEWS AND KRETSINGER (J.MOL.BIOL.(1975)91, 201-228)
Bsol: 130 Å2 / ksol: 0.83 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 8 411 6951
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0167160.4
X-RAY DIFFRACTIONt_angle_deg1.290720.6
X-RAY DIFFRACTIONt_dihedral_angle_d15.638921.2
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0151800.65
X-RAY DIFFRACTIONt_gen_planes0.0169682.2
X-RAY DIFFRACTIONt_it1.667003.4
X-RAY DIFFRACTIONt_nbd0.11421572
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.61.2
X-RAY DIFFRACTIONt_plane_restr0.0162.2

+
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