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- PDB-4b32: Humanised monomeric RadA in complex with napht-1-ol -

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Basic information

Entry
Database: PDB / ID: 4b32
TitleHumanised monomeric RadA in complex with napht-1-ol
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
naphthalen-2-ol / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 20, 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)25,7413
Polymers25,5021
Non-polymers2392
Water5,495305
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.690, 79.050, 39.620
Angle α, β, γ (deg.)90.00, 117.88, 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CONTAINING PUBS520 / 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-03V / naphthalen-2-ol / 2-Naphtol


Mass: 144.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.88 % / 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: I04 / Wavelength: 0.9728
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9728 Å / Relative weight: 1
ReflectionResolution: 1.5→39.53 Å / Num. obs: 32695 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.082 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.36
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 98.8

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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: 1.5→33.064 Å / SU ML: 0.17 / σ(F): 2.01 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1686 5.2 %
Rwork0.1891 --
obs0.1911 32683 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.717 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6366 Å20 Å22.7944 Å2
2--0.0232 Å20 Å2
3----1.6599 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 16 305 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061772
X-RAY DIFFRACTIONf_angle_d1.5772393
X-RAY DIFFRACTIONf_dihedral_angle_d17.805661
X-RAY DIFFRACTIONf_chiral_restr0.148273
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.54440.27761440.25192531X-RAY DIFFRACTION98
1.5444-1.59420.2941550.23172579X-RAY DIFFRACTION100
1.5942-1.65120.25691440.23512576X-RAY DIFFRACTION100
1.6512-1.71730.28051290.21872601X-RAY DIFFRACTION100
1.7173-1.79550.27091410.2082588X-RAY DIFFRACTION100
1.7955-1.89010.24031450.20062575X-RAY DIFFRACTION100
1.8901-2.00850.23271310.18932591X-RAY DIFFRACTION100
2.0085-2.16360.21881550.18692535X-RAY DIFFRACTION100
2.1636-2.38130.21981330.18062619X-RAY DIFFRACTION100
2.3813-2.72570.19271350.18492587X-RAY DIFFRACTION100
2.7257-3.43350.22621340.17832603X-RAY DIFFRACTION100
3.4335-33.07240.19881400.16532612X-RAY DIFFRACTION99

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