[English] 日本語
Yorodumi
- PDB-1f2t: Crystal Structure of ATP-Free RAD50 ABC-ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f2t
TitleCrystal Structure of ATP-Free RAD50 ABC-ATPase
Components(RAD50 ABC-ATPASE) x 2
KeywordsREPLICATION / DNA double-strand break repair / ABC ATPase
Function / homology
Function and homology information


double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHopfner, K.P. / Karcher, A. / Shin, D.S. / Craig, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily.
Authors: Hopfner, K.P. / Karcher, A. / Shin, D.S. / Craig, L. / Arthur, L.M. / Carney, J.P. / Tainer, J.A.
History
DepositionMay 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAD50 ABC-ATPASE
B: RAD50 ABC-ATPASE


Theoretical massNumber of molelcules
Total (without water)33,8982
Polymers33,8982
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-25 kcal/mol
Surface area14320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.57, 67.08, 70.06
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RAD50 ABC-ATPASE


Mass: 17110.840 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#2: Protein RAD50 ABC-ATPASE


Mass: 16787.430 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / References: UniProt: P58301
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM ammonium acetate, 50 mM cacodylate, 10 mM MgCl2, 10% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMNa-phosphate1drop
3300 mM1dropNaCl
41 mMEDTA1drop
5200 mMammonium acetate1reservoir
650 mMcacodylate1reservoir
710 mM1reservoirMgCl2
810 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 567133 / Num. obs: 567133 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.6
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.366 / % possible all: 98.6
Reflection
*PLUS
Num. obs: 46541
Reflection shell
*PLUS
% possible obs: 98.6 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2034 -random 5%
Rwork0.187 ---
all0.187 40425 --
obs0.187 38391 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 0 419 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.01

+
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