[English] 日本語
Yorodumi
- PDB-2cdy: Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cdy
TitleManganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans
ComponentsSUPEROXIDE DISMUTASE [MN]
KeywordsOXIDOREDUCTASE / MANGANESE SUPEROXIDE DISMUTASE / DEINOCOCCUS RADIODURANS / RADIATION RESISTANCE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding / 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 / 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
: / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDennis, R. / Micossi, E. / McCarthy, J. / Moe, E. / Gordon, E. / Leonard, G. / McSweeney, S.
CitationJournal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2006
Title: Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms.
Authors: Dennis, R.J. / Micossi, E. / McCarthy, J. / Moe, E. / Gordon, E.J. / Kozielski-Stuhrmann, S. / Leonard, G.A. / McSweeney, S.
History
DepositionJan 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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

-
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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1518
Polymers103,9324
Non-polymers2204
Water10,215567
1
A: SUPEROXIDE DISMUTASE [MN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0382
Polymers25,9831
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SUPEROXIDE DISMUTASE [MN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0382
Polymers25,9831
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SUPEROXIDE DISMUTASE [MN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0382
Polymers25,9831
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: SUPEROXIDE DISMUTASE [MN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0382
Polymers25,9831
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.577, 87.100, 116.418
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.795, 0.139, -0.59), (0.136, -0.99, -0.049), (-0.591, -0.041, -0.806)51.55883, 75.63525, 174.25024
2given(0.99, 0.141, 0.025), (-0.099, 0.804, -0.587), (-0.103, 0.578, 0.809)-29.81303, 60.49112, -59.54546
3given(0.791, -0.059, -0.608), (0.329, -0.798, 0.505), (-0.515, -0.6, -0.612)38.20346, 14.55108, 119.46127

-
Components

#1: Protein
SUPEROXIDE DISMUTASE [MN] / MNSOD


Mass: 25982.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9RUV2, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CRYSTALLISED CONTAINS AN N-TERMINAL PURIFICATION TAG. WHERE RESIDUES FROM THIS ARE ...THE SEQUENCE CRYSTALLISED CONTAINS AN N-TERMINAL PURIFICATION TAG. WHERE RESIDUES FROM THIS ARE SEEN IN THE CRYSTAL THE NUMBERING IS -1, -2 ETC...

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: DATA COMPLETENESS OF RANGE 41.2-2.25A IS 95.4%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→41.2 Å / Num. obs: 48281 / % possible obs: 82.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9 / % possible all: 41.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CE4 (MONOMER A)

2ce4


Resolution: 2→41.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.833 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO POOR ELECTRON DENSITY THE SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE BEEN TRUNCATED AT CB LYS A142, LYS A210, GLU B46, ASP B105, GLN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO POOR ELECTRON DENSITY THE SIDE CHAINS OF THE FOLLOWING RESIDUES HAVE BEEN TRUNCATED AT CB LYS A142, LYS A210, GLU B46, ASP B105, GLN B91, LYS C210, LYS D139 DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF GLU D158 HAS BEEN TRUNCATED AT CG. DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF MET B23 HAS BEEN TRUNCATED AT SD. DUE TO POOR ELECTRON DENSITY THE SIDE CHAIN OF ASN C94 HAS BEEN TRUNCATED AT CA.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2483 5.1 %RANDOM
Rwork0.173 ---
obs0.176 45779 82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.92 Å2
2--0.51 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6478 0 4 567 7049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216657
X-RAY DIFFRACTIONr_bond_other_d0.0010.025710
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9149060
X-RAY DIFFRACTIONr_angle_other_deg0.797313266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01124.737342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42615988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
X-RAY DIFFRACTIONr_nbd_refined0.2010.21534
X-RAY DIFFRACTIONr_nbd_other0.1780.25744
X-RAY DIFFRACTIONr_nbtor_refined0.180.23273
X-RAY DIFFRACTIONr_nbtor_other0.0850.23392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.54224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16126522
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51332875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3214.52538
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 74
Rwork0.184 1600

+
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