[English] 日本語
Yorodumi
- PDB-3kky: Structure of Manganese Superoxide Dismutase from Deinococcus Radi... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3kky
TitleStructure of Manganese Superoxide Dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity
ComponentsSuperoxide dismutase [Mn]
KeywordsMETAL BINDING PROTEIN / Superoxide dismutase / deinococcus radiodurans / Manganese / Metal-binding / Oxidoreductase
Function / homology
Function and homology information


ec:1.15.1.1: / superoxide dismutase activity / metal ion binding
Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, binding site / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, alpha-hairpin domain / Iron/manganese superoxide dismutases, C-terminal domain / Manganese and iron superoxide dismutases signature.
Superoxide dismutase [Mn]
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGovindasamy, L. / Mikulski, R. / McKenna, M.A. / Silverman, D.N. / McKenna, R.
CitationJournal: To be Published
Title: Structure of Manganese Superoxide dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity
Authors: Govindasamy, L. / Mikulski, R. / McKenna, M.A. / Silverman, D.N. / McKenna, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2009 / Release: Nov 3, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 3, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1184
Polymers47,0082
Non-polymers1102
Water2,918162
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-11 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.15, 80.24, 85.41
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Superoxide dismutase [Mn] / MnSOD


Mass: 23504.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: sodA, DR_1279 / Plasmid: pet31f1(-) / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 / References: UniProt: Q9RUV2, EC: 1.15.1.1
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Manganese
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M K2PO4, 16% PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: osmic
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 34999 / % possible obs: 90 % / Redundancy: 24.8 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.385 / Num. unique all: 3527 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ce4
Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.208 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1758 5 %RANDOM
Rwork0.166 ---
Obs0.166 34999 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 2 162 3392
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0140.0213359
r_angle_refined_deg1.3551.9174577
r_dihedral_angle_1_deg5.3015416
r_dihedral_angle_2_deg36.30924.831178
r_dihedral_angle_3_deg14.85715516
r_dihedral_angle_4_deg16.8481515
r_chiral_restr0.1270.2474
r_gen_planes_refined0.0060.022671
r_nbd_refined0.1910.21334
r_nbtor_refined0.3030.22319
r_xyhbond_nbd_refined0.1030.2122
r_symmetry_vdw_refined0.2290.219
r_symmetry_hbond_refined0.9650.23
r_mcbond_it0.9941.52100
r_mcangle_it1.63623270
r_scbond_it2.46831470
r_scangle_it3.9024.51303
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 127 -
Rwork0.182 2434 -
Obs--91.4 %

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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