[English] 日本語
Yorodumi
- PDB-3qkr: Mre11 Rad50 binding domain bound to Rad50 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qkr
TitleMre11 Rad50 binding domain bound to Rad50
Components
  • (DNA double-strand break repair rad50 ATPase) x 2
  • DNA double-strand break repair protein mre11
KeywordsREPLICATION / RecA-like fold / coiled-coils / ATPase / exonuclease / endonuclease / ATP binding / DNA binding
Function / homology
Function and homology information


DNA end binding / Y-form DNA binding / DNA double-strand break processing / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity ...DNA end binding / Y-form DNA binding / DNA double-strand break processing / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / : / : / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / : / : / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / AAA domain, putative AbiEii toxin, Type IV TA system / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / : / Mre11 nuclease, N-terminal metallophosphatase domain / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA double-strand break repair Rad50 ATPase / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWilliams, G.J. / Williams, R.S. / Arvai, A. / Moncalian, G. / Tainer, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.
Authors: Williams, G.J. / Williams, R.S. / Williams, J.S. / Moncalian, G. / Arvai, A.S. / Limbo, O. / Guenther, G. / Sildas, S. / Hammel, M. / Russell, P. / Tainer, J.A.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA double-strand break repair rad50 ATPase
B: DNA double-strand break repair rad50 ATPase
C: DNA double-strand break repair protein mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4225
Polymers48,2323
Non-polymers1902
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-76 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.041, 116.041, 109.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein DNA double-strand break repair rad50 ATPase / Rad50 ABC-ATPase


Mass: 23615.232 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rad50, PF1167 / Production host: Escherichia coli (E. coli)
References: UniProt: P58301, Hydrolases; Acting on acid anhydrides
#2: Protein DNA double-strand break repair rad50 ATPase / Rad50 ABC-ATPase


Mass: 20553.785 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 704-882)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rad50, PF1167 / Production host: Escherichia coli (E. coli)
References: UniProt: P58301, Hydrolases; Acting on acid anhydrides
#3: Protein/peptide DNA double-strand break repair protein mre11 / Mre11 Nuclease / pfMre11


Mass: 4062.568 Da / Num. of mol.: 1 / Fragment: Rad50 binding domain (UNP residues 348-381)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: mre11, PF1166 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U1N9, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 200-300 mM lithium sulfate, 12-13% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97591
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2003
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHOROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97591 Å / Relative weight: 1
ReflectionResolution: 3.4→100 Å / Num. all: 11608 / Num. obs: 10679 / % possible obs: 91.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.2
Reflection shellResolution: 3.4→3.488 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2 / % possible all: 56.39

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1II8

1ii8


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.871 / SU B: 22.309 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27444 514 4.8 %RANDOM
Rwork0.21129 ---
obs0.21432 10142 91.63 %-
all-11648 --
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: 99.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 10 7 3356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223412
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9834577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30623.899159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.62115683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471527
X-RAY DIFFRACTIONr_chiral_restr0.0690.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022476
X-RAY DIFFRACTIONr_nbd_refined0.230.21729
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.26
X-RAY DIFFRACTIONr_mcbond_it19.8481.52100
X-RAY DIFFRACTIONr_mcangle_it26.93723302
X-RAY DIFFRACTIONr_scbond_it40.05531449
X-RAY DIFFRACTIONr_scangle_it50.8884.51275
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 24 -
Rwork0.266 457 -
obs--56.39 %

+
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