[English] 日本語
Yorodumi
- PDB-3dte: Crystal structure of the IRRE protein, a central regulator of DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dte
TitleCrystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae
ComponentsIrrE protein
KeywordsGENE REGULATION / Deinococcus / Radiotolerance / Metallopeptidase / IrrE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
IrrE, HTH domain / Arc Repressor Mutant, subunit A - #2910 / irre protein / IrrE, HTH domain / : / IrrE N-terminal-like domain / IrrE N-terminal-like domain / LacI-type HTH domain signature. / Beta-Lactamase / Neutral zinc metallopeptidases, zinc-binding region signature. ...IrrE, HTH domain / Arc Repressor Mutant, subunit A - #2910 / irre protein / IrrE, HTH domain / : / IrrE N-terminal-like domain / IrrE N-terminal-like domain / LacI-type HTH domain signature. / Beta-Lactamase / Neutral zinc metallopeptidases, zinc-binding region signature. / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Radiation response metalloprotease IrrE / Radiation response metalloprotease IrrE
Similarity search - Component
Biological speciesDeinococcus deserti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsVujicic-Zagar, A. / Dulermo, R. / Le Gorrec, M. / Vannier, F. / Servant, P. / Sommer, S. / De Groot, A. / Serre, L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae
Authors: Vujicic-Zagar, A. / Dulermo, R. / Le Gorrec, M. / Vannier, F. / Servant, P. / Sommer, S. / de Groot, A. / Serre, L.
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IrrE protein


Theoretical massNumber of molelcules
Total (without water)32,7121
Polymers32,7121
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: IrrE protein

A: IrrE protein


Theoretical massNumber of molelcules
Total (without water)65,4252
Polymers65,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.053, 52.813, 64.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein IrrE protein


Mass: 32712.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: irrE / Plasmid: PET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5B9W8, UniProt: C1CZ84*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG 3350, 0.2M Potassium Fluoride, pH 7.5, VAPOR DIFFUSION, temperature 281K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 9581 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.129
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 11.7 % / Rsym value: 0.43 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.581 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.676 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25415 456 4.8 %RANDOM
Rwork0.21825 ---
obs0.21991 9097 99.99 %-
all-9581 --
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: 43.615 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2---1.52 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 0 49 1922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221912
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9862602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41422.28983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48315299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4851521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021467
X-RAY DIFFRACTIONr_nbd_refined0.2740.2834
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.26
X-RAY DIFFRACTIONr_mcbond_it1.61421267
X-RAY DIFFRACTIONr_mcangle_it2.23231975
X-RAY DIFFRACTIONr_scbond_it1.5612708
X-RAY DIFFRACTIONr_scangle_it2.1843627
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 30 -
Rwork0.269 634 -
obs--100 %

+
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