[English] 日本語
Yorodumi
- PDB-4b3b: Humanised monomeric RadA in complex with FHTA tetrapeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b3b
TitleHumanised monomeric RadA in complex with FHTA tetrapeptide
Components
  • DNA REPAIR AND RECOMBINATION PROTEIN RADA
  • FHTA TETRAPEPTIDE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / RECOMBINASE / THERMOSTABLE / HUMANISED / PEPTIDE-BINDING
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
PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.193 Å
AuthorsScott, D.E. / Ehebauer, M.T. / Pukala, T. / Marsh, M. / Blundell, T.L. / Venkitaraman, A.R. / Abell, C. / Hyvonen, M.
CitationJournal: Chembiochem / Year: 2013
Title: Using a Fragment-Based Approach to Target Protein-Protein Interactions.
Authors: Scott, D.E. / Ehebauer, M.T. / Pukala, T. / Marsh, M. / Blundell, T.L. / Venkitaraman, A.R. / Abell, C. / Hyvonen, M.
History
DepositionJul 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA REPAIR AND RECOMBINATION PROTEIN RADA
C: FHTA TETRAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0973
Polymers26,0022
Non-polymers951
Water5,747319
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-12.4 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.227, 60.589, 87.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA REPAIR AND RECOMBINATION PROTEIN RADA


Mass: 25502.150 Da / Num. of mol.: 1 / Fragment: ATPASE, RESIDUES 108-287,300-349 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CONTAINING PUBS520 PLASMID / References: UniProt: O74036
#2: Protein/peptide FHTA TETRAPEPTIDE


Mass: 499.563 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF BRC4 REPEAT OF BRCA2 / Source method: obtained synthetically / Details: ACETYLATED N-TERMINUS AND AMIDATED C-TERMINUS / Source: (synth.) HOMO SAPIENS (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 169 TO MET ENGINEERED RESIDUE IN CHAIN A, TYR 201 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ILE 169 TO MET ENGINEERED RESIDUE IN CHAIN A, TYR 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 202 TO TYR ENGINEERED RESIDUE IN CHAIN A, LYS 221 TO MET ENGINEERED RESIDUE IN CHAIN A, ASN 300 TO ILE
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.03 % / Description: NONE
Crystal growpH: 6.2 / Details: pH 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.19→26.29 Å / Num. obs: 64405 / % possible obs: 93.4 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Biso Wilson estimate: 8.39 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.06
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.14 / % possible all: 90.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PZN CHAIN A

1pzn


Resolution: 1.193→26.286 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 12.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 3251 5.1 %
Rwork0.14 --
obs0.1414 64403 93.44 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.653 Å2 / ksol: 0.489 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2999 Å20 Å20 Å2
2--1.1044 Å20 Å2
3----2.4043 Å2
Refinement stepCycle: LAST / Resolution: 1.193→26.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 5 319 2106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011927
X-RAY DIFFRACTIONf_angle_d1.3972612
X-RAY DIFFRACTIONf_dihedral_angle_d13.387734
X-RAY DIFFRACTIONf_chiral_restr0.074295
X-RAY DIFFRACTIONf_plane_restr0.006346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1925-1.21030.23371150.19662162X-RAY DIFFRACTION76
1.2103-1.22920.19441650.16632610X-RAY DIFFRACTION95
1.2292-1.24940.16461590.13572705X-RAY DIFFRACTION97
1.2494-1.27090.15421350.12332702X-RAY DIFFRACTION97
1.2709-1.2940.16461480.12452721X-RAY DIFFRACTION96
1.294-1.31890.15561410.12272735X-RAY DIFFRACTION97
1.3189-1.34580.15781530.12212727X-RAY DIFFRACTION96
1.3458-1.37510.1621390.11682725X-RAY DIFFRACTION98
1.3751-1.40710.13531460.11332708X-RAY DIFFRACTION96
1.4071-1.44230.16571350.11652747X-RAY DIFFRACTION97
1.4423-1.48130.15131570.1132738X-RAY DIFFRACTION97
1.4813-1.52480.14421480.10562693X-RAY DIFFRACTION96
1.5248-1.57410.13431340.10682733X-RAY DIFFRACTION96
1.5741-1.63030.14711310.10692744X-RAY DIFFRACTION96
1.6303-1.69560.14761260.11482753X-RAY DIFFRACTION96
1.6956-1.77270.16771380.1232699X-RAY DIFFRACTION95
1.7727-1.86620.14911280.13242725X-RAY DIFFRACTION95
1.8662-1.98310.21031280.13152680X-RAY DIFFRACTION94
1.9831-2.13610.14951660.13852659X-RAY DIFFRACTION93
2.1361-2.35090.15441460.13652636X-RAY DIFFRACTION92
2.3509-2.69080.17391370.15582618X-RAY DIFFRACTION90
2.6908-3.3890.18961610.15962568X-RAY DIFFRACTION88
3.389-26.29240.18151150.18432364X-RAY DIFFRACTION77

+
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