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- PDB-5fow: HUMANISED MONOMERIC RADA IN COMPLEX WITH WHTA TETRAPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fow
TitleHUMANISED MONOMERIC RADA IN COMPLEX WITH WHTA TETRAPEPTIDE
Components
  • DNA repair and recombination protein RadA
  • WHTA 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: 1.797 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
Revision 2.0Jun 19, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / diffrn_source ...atom_site / diffrn_source / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_biol / struct_conf / struct_conn / struct_ref / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.auth_seq_id / _pdbx_solvent_atom_site_mapping.label_asym_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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 / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _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_beg / _struct_ref_seq.seq_align_end / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Revision 2.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2716
Polymers52,0814
Non-polymers1902
Water10,755597
1
A: DNA repair and recombination protein RadA
E: WHTA PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1363
Polymers26,0412
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area10700 Å2
MethodPISA
2
C: DNA repair and recombination protein RadA
F: WHTA PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1363
Polymers26,0412
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.479, 87.598, 61.938
Angle α, β, γ (deg.)90.00, 92.37, 90.00
Int Tables number4
Space group name H-MP1211

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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 WHTA PEPTIDE


Mass: 538.599 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMENT OF LOOP 287-300 BY AN N.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.1 % / Description: NONE
Crystal growpH: 6.2 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97952
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.8→33.23 Å / Num. obs: 38505 / % possible obs: 95.7 % / Observed criterion σ(I): 3 / Redundancy: 2.79 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.96
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.05 / % possible all: 93.5

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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: 1.797→33.232 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1979 5.1 %
Rwork0.1829 --
obs0.1847 38500 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.797→33.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 12 597 4103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063608
X-RAY DIFFRACTIONf_angle_d0.8084869
X-RAY DIFFRACTIONf_dihedral_angle_d30.0331368
X-RAY DIFFRACTIONf_chiral_restr0.056553
X-RAY DIFFRACTIONf_plane_restr0.004632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.797-1.8420.28241400.22312502X-RAY DIFFRACTION92
1.842-1.89180.30681300.21962602X-RAY DIFFRACTION96
1.8918-1.94740.26431350.21082558X-RAY DIFFRACTION95
1.9474-2.01030.24511250.19392609X-RAY DIFFRACTION95
2.0103-2.08210.26331540.18872578X-RAY DIFFRACTION96
2.0821-2.16550.21861430.18312603X-RAY DIFFRACTION95
2.1655-2.2640.22991360.17662606X-RAY DIFFRACTION96
2.264-2.38330.22561470.1812606X-RAY DIFFRACTION96
2.3833-2.53260.22391350.18322629X-RAY DIFFRACTION96
2.5326-2.72810.24621540.18942621X-RAY DIFFRACTION97
2.7281-3.00250.21221360.19592652X-RAY DIFFRACTION97
3.0025-3.43650.21541340.1762647X-RAY DIFFRACTION96
3.4365-4.32820.16381590.1542620X-RAY DIFFRACTION97
4.3282-33.23760.19331510.1782688X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2380.48340.01881.26670.19390.7401-0.0225-0.05030.0056-0.02090.0070.0277-0.0578-0.03380.00950.05790.0124-0.00010.0740.0020.04931.7918-0.25360.0625
21.3620.40560.13341.0833-0.15181.0628-0.0059-0.06460.00070.02080.0013-0.04140.04340.05860.00220.0520.02040.00130.0623-0.00870.049220.749224.2334-30.9206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN C

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