[English] 日本語
Yorodumi
- PDB-5lbi: Apo-structure of humanised RadA-mutant humRadA3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lbi
TitleApo-structure of humanised RadA-mutant humRadA3
ComponentsDNA repair and recombination protein RadA
KeywordsHYDROLASE / DNA repair / fragment based drug design / humanisation
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
DNA recombination/repair protein RadA / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein RadA / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMarsh, M. / Fischer, G. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Marsh, M. / Fischer, G. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. / Blundell, T.L. / Hyvonen, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51.
Authors: Moschetti, T. / Sharpe, T. / Fischer, G. / Marsh, M.E. / Ng, H.K. / Morgan, M. / Scott, D.E. / Blundell, T.L. / R Venkitaraman, A. / Skidmore, J. / Abell, C. / Hyvonen, M.
History
DepositionJun 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5082
Polymers25,4681
Non-polymers401
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.350, 77.980, 39.810
Angle α, β, γ (deg.)90.00, 117.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA repair and recombination protein RadA / humRadA3


Mass: 25468.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: radA, PF1926 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 4-8% PEG1000, 100 mM Na/KPO4, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.43→40 Å / Num. obs: 36018 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.045 / Net I/σ(I): 20.51
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.56 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A6P

4a6p


Resolution: 1.43→35.3 Å / Cor.coef. Fo:Fc: 0.9602 / Cor.coef. Fo:Fc free: 0.9486 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1798 4.99 %RANDOM
Rwork0.1638 ---
obs0.1652 36017 96.51 %-
Displacement parametersBiso mean: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.255 Å20 Å2-1.8795 Å2
2---1.146 Å20 Å2
3---1.401 Å2
Refinement stepCycle: 1 / Resolution: 1.43→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 1 270 3714
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013471HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116288HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes520HARMONIC5
X-RAY DIFFRACTIONt_it3471HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.24
X-RAY DIFFRACTIONt_other_torsion16.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion229SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4054SEMIHARMONIC4
LS refinement shellResolution: 1.43→1.47 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2078 117 5.15 %
Rwork0.2134 2155 -
all0.213 2272 -
obs--96.51 %

+
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