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- PDB-2h8c: Structure of RusA D70N in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 2h8c
TitleStructure of RusA D70N in complex with DNA
Components
  • 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
  • Crossover junction endodeoxyribonuclease rusA
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / RECOMBINATION / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / four-way junction DNA binding / DNA recombination / DNA repair / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Holliday junction resolvase RusA / Holliday junction resolvase RusA-like / Crossover junction endodeoxyribonuclease, RusA / Holliday junction resolvase RusA-like superfamily / Endodeoxyribonuclease RusA / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Crossover junction endodeoxyribonuclease RusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMacmaster, R.A.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity.
Authors: Macmaster, R. / Sedelnikova, S. / Baker, P.J. / Bolt, E.L. / Lloyd, R.G. / Rafferty, J.B.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
Z: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
W: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
X: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
A: Crossover junction endodeoxyribonuclease rusA
B: Crossover junction endodeoxyribonuclease rusA
C: Crossover junction endodeoxyribonuclease rusA
D: Crossover junction endodeoxyribonuclease rusA


Theoretical massNumber of molelcules
Total (without water)68,8698
Polymers68,8698
Non-polymers00
Water362
1
W: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
X: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
A: Crossover junction endodeoxyribonuclease rusA
B: Crossover junction endodeoxyribonuclease rusA


Theoretical massNumber of molelcules
Total (without water)34,4344
Polymers34,4344
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
Z: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
C: Crossover junction endodeoxyribonuclease rusA
D: Crossover junction endodeoxyribonuclease rusA


Theoretical massNumber of molelcules
Total (without water)34,4344
Polymers34,4344
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.616, 59.483, 90.721
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'


Mass: 3350.185 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Crossover junction endodeoxyribonuclease rusA / Holliday junction nuclease rusA / Holliday junction resolvase


Mass: 13866.949 Da / Num. of mol.: 4 / Mutation: D70N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rusA, rus / Production host: Escherichia coli (E. coli)
References: UniProt: P0AG74, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / pH: 7.1
Details: 20% PEG 3350, 0.2M Sodium Fluoride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.10
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Sodium Fluoride11
3Sodium Fluoride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→44 Å / Num. obs: 12485 / % possible obs: 99.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.27 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q8R

1q8r


Resolution: 3.1→44.46 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.843 / SU B: 66.786 / SU ML: 0.525 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 601 4.8 %RANDOM
Rwork0.247 ---
obs0.249 11874 99.9 %-
all-12485 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å2-0.94 Å2
2--5.26 Å20 Å2
3----8.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 868 0 2 4344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0214561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9222.1976400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0955452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93123.399153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.79215554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.221528
X-RAY DIFFRACTIONr_chiral_restr0.0450.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3040.22393
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.22966
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 45 -
Rwork0.452 850 -
obs--100 %
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)
15.40881.16090.68343.321.5917.89610.030.06290.0449-0.09890.0534-0.38980.18980.9308-0.0834-0.35280.10310.0404-0.2509-0.0356-0.449415.92681.40753.6776
24.145-0.9643-0.38277.1312-2.66149.10830.10240.0822-0.02420.12820.0201-0.3074-0.4992-0.2526-0.12260.0253-0.0495-0.1627-0.14310.1191-0.428741.179617.408752.0249
31.1584-1.338-0.807219.27236.22492.1426-0.0534-0.5642-0.01510.9082-0.24740.56040.1354-0.31660.3007-0.1094-0.0667-0.0732-0.0141-0.1533-0.51465.2621.567622.9458
45.19982.4075-4.1433.908-6.818221.8599-0.36680.4093-0.35910.29850.47930.30430.4728-2.0688-0.11250.2208-0.06230.09870.48920.1837-0.109537.569722.997725.3321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE2 - 1182 - 118
2X-RAY DIFFRACTION1BF2 - 1172 - 117
3X-RAY DIFFRACTION2CG2 - 1182 - 118
4X-RAY DIFFRACTION2DH2 - 1182 - 118
5X-RAY DIFFRACTION3WC2 - 121 - 11
6X-RAY DIFFRACTION3XD2 - 121 - 11
7X-RAY DIFFRACTION4YA2 - 121 - 11
8X-RAY DIFFRACTION4ZB2 - 111 - 10

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