[English] 日本語
Yorodumi
- PDB-5fov: HUMANISED MONOMERIC RADA IN COMPLEX WITH FHTG TETRAPEPTIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fov
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH FHTG TETRAPEPTIDE
Components
  • DNA repair and recombination protein RadA
  • FHTG PEPTIDE
KeywordsHYDROLASE / RADA / FXXA MOTIF / RECOMBINASE
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.739 Å
AuthorsScott, D.E. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structure Activity Relationship of the Peptide Binding Motif Mediating the Rad51:Brca2 Protein-Protein Interaction.
Authors: Scott, D.E. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M.
History
DepositionNov 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3May 2, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.0Jun 19, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_solvent_atom_site_mapping.label_asym_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_seq_id_1 / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.sheet_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair and recombination protein RadA
C: DNA repair and recombination protein RadA
E: FHTG PEPTIDE
F: FHTG PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2577
Polymers51,9754
Non-polymers2823
Water11,422634
1
A: DNA repair and recombination protein RadA
E: FHTG PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0833
Polymers25,9882
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13.9 kcal/mol
Surface area10910 Å2
MethodPISA
2
C: DNA repair and recombination protein RadA
F: FHTG PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1754
Polymers25,9882
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13.3 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.334, 87.233, 61.543
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25502.150 Da / Num. of mol.: 2 / Fragment: ATPASE, UNP RESIDUES 108-349 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 / References: UniProt: O74036
#2: Protein/peptide FHTG PEPTIDE


Mass: 485.537 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: ACETYLATED AT THE N-TERMINUS AND AMIDATED IN THE C-TERMINUS
Source: (synth.) HOMO SAPIENS (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMENT OF LOOP 287-300 BY AN N.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42.1 % / Description: NONE
Crystal growpH: 6.2 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.73→61.49 Å / Num. obs: 42203 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.56 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.07
Reflection shellResolution: 1.73→1.84 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.75 / % possible all: 83.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B3B

4b3b


Resolution: 1.739→43.617 Å / SU ML: 0.2 / σ(F): 0.92 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 4013 5.2 %
Rwork0.176 --
obs0.1781 42189 90.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.739→43.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 20 634 4205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063704
X-RAY DIFFRACTIONf_angle_d0.9455004
X-RAY DIFFRACTIONf_dihedral_angle_d13.8131397
X-RAY DIFFRACTIONf_chiral_restr0.04564
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7386-1.75910.37590.2839899X-RAY DIFFRACTION31
1.7591-1.78050.23041100.26052450X-RAY DIFFRACTION87
1.7805-1.8030.28561400.25912455X-RAY DIFFRACTION88
1.803-1.82680.2861320.24342485X-RAY DIFFRACTION86
1.8268-1.85180.29151360.24162479X-RAY DIFFRACTION88
1.8518-1.87830.24721320.24162488X-RAY DIFFRACTION89
1.8783-1.90630.29991270.22682522X-RAY DIFFRACTION89
1.9063-1.93610.26521250.22182524X-RAY DIFFRACTION89
1.9361-1.96780.21031330.21282568X-RAY DIFFRACTION91
1.9678-2.00180.27671150.21562577X-RAY DIFFRACTION91
2.0018-2.03810.25761460.20662580X-RAY DIFFRACTION92
2.0381-2.07740.24091430.19452563X-RAY DIFFRACTION92
2.0774-2.11980.26321150.1922687X-RAY DIFFRACTION92
2.1198-2.16580.25131540.18122536X-RAY DIFFRACTION93
2.1658-2.21620.26161600.17872607X-RAY DIFFRACTION92
2.2162-2.27160.21241530.17512623X-RAY DIFFRACTION93
2.2716-2.33310.17611320.17222671X-RAY DIFFRACTION94
2.3331-2.40170.23791570.15882639X-RAY DIFFRACTION94
2.4017-2.47920.22521610.16712632X-RAY DIFFRACTION95
2.4792-2.56780.21430.16612677X-RAY DIFFRACTION95
2.5678-2.67060.23731730.16982703X-RAY DIFFRACTION95
2.6706-2.79210.18491290.17442652X-RAY DIFFRACTION95
2.7921-2.93930.21911390.17572678X-RAY DIFFRACTION95
2.9393-3.12340.20371370.17152736X-RAY DIFFRACTION95
3.1234-3.36450.1791260.14932670X-RAY DIFFRACTION95
3.3645-3.70290.19241600.14352642X-RAY DIFFRACTION94
3.7029-4.23840.17951350.12862646X-RAY DIFFRACTION95
4.2384-5.33840.16371770.13312620X-RAY DIFFRACTION94
5.3384-43.63020.19021640.17312669X-RAY DIFFRACTION95

+
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