[English] 日本語
Yorodumi
- PDB-6qzn: H30 MnSOD-3 Mutant III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qzn
TitleH30 MnSOD-3 Mutant III
Components(Superoxide dismutase [Mn] 2, mitochondrial) x 2
KeywordsOXIDOREDUCTASE / superoxide / mutation / dismutase
Function / homology
Function and homology information


respiratory chain complex / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / manganese ion binding / protein homodimerization activity / mitochondrion
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / Superoxide dismutase [Mn] 2, mitochondrial
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBonetta, R. / Trinh, C.H. / Hunter, G.J. / Hunter, T.
CitationJournal: To Be Published
Title: H30 MnSOD-3 Mutant II
Authors: Bonetta, R. / Trinh, C.H. / Hunter, G.J. / Hunter, T.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Mn] 2, mitochondrial
C: Superoxide dismutase [Mn] 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8065
Polymers44,6002
Non-polymers2063
Water4,936274
1
A: Superoxide dismutase [Mn] 2, mitochondrial
C: Superoxide dismutase [Mn] 2, mitochondrial
hetero molecules

A: Superoxide dismutase [Mn] 2, mitochondrial
C: Superoxide dismutase [Mn] 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,61110
Polymers89,1994
Non-polymers4126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7940 Å2
ΔGint-60 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.900, 81.900, 137.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21C-346-

HOH

-
Components

#1: Protein Superoxide dismutase [Mn] 2, mitochondrial


Mass: 22234.266 Da / Num. of mol.: 1 / Mutation: H30Q
Source method: isolated from a genetically manipulated source
Details: Residue 128 is S-hydroxycysteine instead of cysteine
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sod-3, C08A9.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41977, superoxide dismutase
#2: Protein Superoxide dismutase [Mn] 2, mitochondrial


Mass: 22365.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 128 is S-hydroxycysteine instead of cysteine
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sod-3, C08A9.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41977, superoxide dismutase
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: bicine ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.09 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 1.64→57.91 Å / Num. obs: 57915 / % possible obs: 99.9 % / Redundancy: 9.3 % / Net I/σ(I): 14.6
Reflection shellResolution: 1.64→1.73 Å / Num. unique obs: 3988

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dc5

3dc5


Resolution: 1.64→57.91 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.779 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22759 2967 5.1 %RANDOM
Rwork0.19855 ---
obs0.20002 54898 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.64→57.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 7 274 3427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193253
X-RAY DIFFRACTIONr_bond_other_d0.0030.023080
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9314409
X-RAY DIFFRACTIONr_angle_other_deg0.95437096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02825.215163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79315565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9621510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023698
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02776
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_it0.7291.5061560
X-RAY DIFFRACTIONr_mcbond_other0.7281.5041559
X-RAY DIFFRACTIONr_mcangle_it1.1552.2531948
X-RAY DIFFRACTIONr_mcangle_other1.1552.2551949
X-RAY DIFFRACTIONr_scbond_it1.0931.6411693
X-RAY DIFFRACTIONr_scbond_other1.091.631690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7062.3842452
X-RAY DIFFRACTIONr_long_range_B_refined5.95113.1814016
X-RAY DIFFRACTIONr_long_range_B_other5.84512.5573899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.641→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 219 -
Rwork0.244 3988 -
obs--99.98 %
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)
11.40590.4878-0.02692.223-1.61833.19770.0123-0.1328-0.0903-0.3587-0.3511-0.43290.56860.42940.33890.15050.04020.06890.1130.08260.190226.5645.885-0.453
21.2083-0.170.56511.2343-0.59482.2096-0.0057-0.3213-0.13360.10650.13880.271-0.0788-0.4735-0.13310.01020.01270.01750.15150.080.1989-8.557-2.44214.095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 194
2X-RAY DIFFRACTION2C0 - 194

+
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