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- PDB-4qkq: RadA from Methanococcus Voltae in complex with copper phthalocyan... -

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Basic information

Entry
Database: PDB / ID: 4qkq
TitleRadA from Methanococcus Voltae in complex with copper phthalocyanine tetrasulfonate inhibitor
ComponentsDNA repair and recombination protein RadA
KeywordsDNA BINDING PROTEIN / RadA / Rad51 / DMC1 / RecA / ATPase / DNA strand Exchange / Homologous Recombination / RECA FOLD / ATP binding / DNA 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 / identical protein 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
Copper(II) tetrapyrrole / NITRATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRao, D.E.C.S. / Li, Y. / He, Y. / Luo, Y.
CitationJournal: To be Published
Title: Crystal Structure of an archaeal Rad51 homolog in complex with a phthalocyanine tetrasulfonate inhibitor
Authors: Rao, D.E.C.S. / Li, Y. / He, Y. / Luo, Y.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Non-polymer description
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: DNA repair and recombination protein RadA
C: DNA repair and recombination protein RadA
D: DNA repair and recombination protein RadA
E: DNA repair and recombination protein RadA
F: DNA repair and recombination protein RadA
G: DNA repair and recombination protein RadA
H: DNA repair and recombination protein RadA
I: DNA repair and recombination protein RadA
J: DNA repair and recombination protein RadA
K: DNA repair and recombination protein RadA
L: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,91943
Polymers352,73112
Non-polymers2,18831
Water8,413467
1
A: DNA repair and recombination protein RadA
B: DNA repair and recombination protein RadA
C: DNA repair and recombination protein RadA
D: DNA repair and recombination protein RadA
E: DNA repair and recombination protein RadA
F: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,42023
Polymers176,3666
Non-polymers1,05417
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16980 Å2
ΔGint-79 kcal/mol
Surface area58410 Å2
MethodPISA
2
G: DNA repair and recombination protein RadA
H: DNA repair and recombination protein RadA
I: DNA repair and recombination protein RadA
J: DNA repair and recombination protein RadA
K: DNA repair and recombination protein RadA
L: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,50020
Polymers176,3666
Non-polymers1,13414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17590 Å2
ΔGint-79 kcal/mol
Surface area58720 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40760 Å2
ΔGint-162 kcal/mol
Surface area110950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.000, 111.000, 112.400
Angle α, β, γ (deg.)112.30, 101.60, 114.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA repair and recombination protein RadA


Mass: 29394.273 Da / Num. of mol.: 12 / Fragment: RadA ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae (archaea) / Gene: radA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+ / References: UniProt: O73948
#2: Chemical...
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-35N / Copper(II) tetrapyrrole


Mass: 327.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16CuN4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2 M NH4NO3, 0.05 M Tris-HCl, 30% ploy(ethylene glycol) monomethyl ester 550, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 13, 2010 / Details: mirrows
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 280610 / Num. obs: 258442 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 29.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.9 / Num. unique all: 20834 / Rsym value: 0.493 / % possible all: 74.2

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Processing

Software
NameClassification
HKL-2000data collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DC9

4dc9


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 11681 -Random
Rwork0.224 ---
all0.224 276881 --
obs0.224 234028 84.5 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23964 0 141 467 24572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.32

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