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- PDB-5fdk: Crystal structure of RecU(D88N) in complex with palindromic DNA duplex -

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Basic information

Entry
Database: PDB / ID: 5fdk
TitleCrystal structure of RecU(D88N) in complex with palindromic DNA duplex
Components
  • Holliday junction resolvase RecU
  • palindromic DNA
KeywordsHYDROLASE / Resolvase / Holliday junction / RecU / DNA / complex / DNA-Binding Proteins
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / chromosome segregation / DNA recombination / endonuclease activity / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Holliday junction resolvase RecU / Recombination protein U / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction resolvase RecU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.208 Å
AuthorsKhavnekar, S. / Rafferty, J.B. / Kale, A.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state.
Authors: Khavnekar, S. / Dantu, S.C. / Sedelnikova, S. / Ayora, S. / Rafferty, J. / Kale, A.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Holliday junction resolvase RecU
B: Holliday junction resolvase RecU
C: Holliday junction resolvase RecU
D: Holliday junction resolvase RecU
E: palindromic DNA
F: palindromic DNA
G: palindromic DNA
H: palindromic DNA


Theoretical massNumber of molelcules
Total (without water)108,2848
Polymers108,2848
Non-polymers00
Water00
1
A: Holliday junction resolvase RecU
C: Holliday junction resolvase RecU
E: palindromic DNA
F: palindromic DNA
G: palindromic DNA
H: palindromic DNA


Theoretical massNumber of molelcules
Total (without water)61,4676
Polymers61,4676
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Holliday junction resolvase RecU
D: Holliday junction resolvase RecU
E: palindromic DNA
F: palindromic DNA

G: palindromic DNA
H: palindromic DNA


Theoretical massNumber of molelcules
Total (without water)61,4676
Polymers61,4676
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_445x-1/3,y-2/3,z+1/31
Unit cell
Length a, b, c (Å)144.447, 144.447, 310.343
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Holliday junction resolvase RecU


Mass: 23408.490 Da / Num. of mol.: 4 / Mutation: D88N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: recU, prfA, yppB, BSU22310 / Plasmid: pCB210 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: P39792, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: DNA chain
palindromic DNA


Mass: 3662.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE pH 9, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.208→116.024 Å / Num. all: 20730 / Num. obs: 20730 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 118.19 Å2 / Rmerge(I) obs: 0.09081 / Rpim(I) all: 0.03 / Rrim(I) all: 0.1 / Rsym value: 0.095 / Net I/av σ(I): 6.385 / Net I/σ(I): 16.7 / Num. measured all: 229929
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.21-3.3811.21.4150.53339629920.441.4151.899.4
3.38-3.5911.30.8410.93189328180.2610.8413.2100
3.59-3.8311.30.4661.63008826710.1450.4666.1100
3.83-4.1411.20.2333.12807524960.0730.23310.9100
4.14-4.5411.20.1116.72571722890.0350.11117.6100
4.54-5.0711.20.0779.42335820940.0240.07724.4100
5.07-5.8611.10.06810.52044318440.0210.06826.7100
5.86-7.1710.90.05911.41726515860.0190.05931.8100
7.17-10.1410.50.03715.31313712530.0120.03747.9100
10.14-48.6949.50.0331865576870.0120.03354.896

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.21 Å48.53 Å
Translation6.33 Å48.53 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.208→48.694 Å / FOM work R set: 0.6869 / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3286 1063 5.13 %
Rwork0.2561 19653 -
obs0.2597 20716 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.77 Å2 / Biso mean: 82.91 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.208→48.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5195 943 943 0 7081
Biso mean--105.23 --
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016367
X-RAY DIFFRACTIONf_angle_d1.6578891
X-RAY DIFFRACTIONf_chiral_restr0.115995
X-RAY DIFFRACTIONf_plane_restr0.0091020
X-RAY DIFFRACTIONf_dihedral_angle_d22.0332184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2076-3.35350.36711560.31122379253599
3.3535-3.53030.3921380.306124352573100
3.5303-3.75140.41981220.288424352557100
3.7514-4.04090.31571290.256124462575100
4.0409-4.44730.35031340.232924542588100
4.4473-5.09030.32851430.239424382581100
5.0903-6.41090.32411140.288425062620100
6.4109-48.70.29211270.23692560268799

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