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- PDB-4b2i: Humanised monomeric RadA in complex with indazole -

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Basic information

Entry
Database: PDB / ID: 4b2i
TitleHumanised monomeric RadA in complex with indazole
ComponentsDNA REPAIR AND RECOMBINATION PROTEIN RADA
KeywordsHYDROLASE / RECOMBINASE / THERMOSTABLE / 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
1H-indazole / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,7153
Polymers25,5021
Non-polymers2132
Water6,197344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.620, 78.770, 39.630
Angle α, β, γ (deg.)90.00, 118.06, 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.: 1 / Fragment: ATPASE, RESIDUES 108-349 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CONTAINING PUBS520 PLASMID / References: UniProt: O74036
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-LZ1 / 1H-indazole


Mass: 118.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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, ILE 300 TO ASN
Sequence detailsDELETION 1-107,HUMANISING MUTATIONS I169M,Y201A, V202Y,K221M,I300N, LOOP DELETION 288-299, I300N

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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: 2.03 Å3/Da / Density % sol: 39.46 % / Description: NONE
Crystal growpH: 6.2 / Details: 10-15% PEG-1000, 50 MM NAKPHOSPHATE, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→39.38 Å / Num. obs: 49540 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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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 1PZN CHAIN A

1pzn


Resolution: 1.3→33.064 Å / SU ML: 0.15 / σ(F): 2 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 2552 5.2 %
Rwork0.1993 --
obs0.2005 49527 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.964 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4549 Å20 Å22.3241 Å2
2--0.651 Å20 Å2
3----2.1059 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 14 344 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061772
X-RAY DIFFRACTIONf_angle_d1.5492392
X-RAY DIFFRACTIONf_dihedral_angle_d17.699662
X-RAY DIFFRACTIONf_chiral_restr0.153272
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32510.27441300.28612595X-RAY DIFFRACTION98
1.3251-1.35220.31760.2732555X-RAY DIFFRACTION100
1.3522-1.38160.28231280.26992646X-RAY DIFFRACTION100
1.3816-1.41370.27721170.25562643X-RAY DIFFRACTION100
1.4137-1.4490.25121510.25092618X-RAY DIFFRACTION99
1.449-1.48820.25711380.23692602X-RAY DIFFRACTION100
1.4882-1.5320.25381520.23462616X-RAY DIFFRACTION100
1.532-1.58150.23231610.22562621X-RAY DIFFRACTION100
1.5815-1.6380.26621400.22172615X-RAY DIFFRACTION100
1.638-1.70360.20871340.2212622X-RAY DIFFRACTION100
1.7036-1.78110.2831560.20212592X-RAY DIFFRACTION100
1.7811-1.8750.22011380.20392651X-RAY DIFFRACTION99
1.875-1.99250.24851250.1962627X-RAY DIFFRACTION99
1.9925-2.14630.21941640.18252587X-RAY DIFFRACTION99
2.1463-2.36220.21421340.1822635X-RAY DIFFRACTION99
2.3622-2.70390.20211320.1932644X-RAY DIFFRACTION99
2.7039-3.4060.20141430.18012641X-RAY DIFFRACTION100
3.406-33.07480.19581330.17752465X-RAY DIFFRACTION92

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