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- PDB-1q8r: Structure of E.coli RusA Holliday junction resolvase -

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Basic information

Entry
Database: PDB / ID: 1q8r
TitleStructure of E.coli RusA Holliday junction resolvase
ComponentsCrossover junction endodeoxyribonuclease rusA
KeywordsRECOMBINATION / HYDROLASE / extended mixed beta sheet / chorismate mutase-like fold
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / 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
Crossover junction endodeoxyribonuclease RusA / Crossover junction endodeoxyribonuclease RusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.899 Å
AuthorsRafferty, J.B. / Bolt, E.L. / Muranova, T.A. / Sedelnikova, S.E. / Leonard, P. / Pasquo, A. / Baker, P.J. / Rice, D.W. / Sharples, G.J. / Lloyd, R.G.
CitationJournal: Structure / Year: 2003
Title: The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold
Authors: Rafferty, J.B. / Bolt, E.L. / Muranova, T.A. / Sedelnikova, S.E. / Leonard, P. / Pasquo, A. / Baker, P.J. / Rice, D.W. / Sharples, G.J. / Lloyd, R.G.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crossover junction endodeoxyribonuclease rusA
B: Crossover junction endodeoxyribonuclease rusA


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,7362
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.352, 50.052, 49.597
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRAA1 - 171 - 17
21METMETTYRTYRBB1 - 171 - 17
32GLUGLUGLYGLYAA30 - 11830 - 118
42GLUGLUGLYGLYBB30 - 11830 - 118
DetailsThe asymmetric unit contains the biologically active dimer

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Components

#1: Protein Crossover junction endodeoxyribonuclease rusA / E.C.3.1.22.- / RusA resolvase / Holliday junction nuclease rusA / Holliday junction resolvase / endodeoxyribonuclease RUS


Mass: 13867.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rusa / Plasmid: pEB259 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P40116, UniProt: P0AG74*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, sodium acetate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
230 %PEG40001reservoir
30.3 Msodium acetate1reservoirin Tris-HCl, pH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001
Details: tungsten carbide primary slits, Si crystal monochromator, tungsten carbide secondary slits, toroidal zerodur mirror
RadiationMonochromator: Si crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. all: 17267 / Num. obs: 17267 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.036 / Net I/σ(I): 12.25
Reflection shellResolution: 1.899→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1028 / Mean I/σ(I) obs: 8.58 / Num. unique all: 1258 / Rsym value: 0.151 / % possible all: 97
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 97 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.899→48.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.615 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22622 868 5 %RANDOM
Rwork0.19011 ---
all0.231 17267 --
obs0.19199 16398 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.064 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20.01 Å2
2---0.99 Å20 Å2
3---3.32 Å2
Refinement stepCycle: LAST / Resolution: 1.899→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 131 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221790
X-RAY DIFFRACTIONr_bond_other_d0.0020.021674
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9532428
X-RAY DIFFRACTIONr_angle_other_deg0.74233867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265224
X-RAY DIFFRACTIONr_chiral_restr0.0890.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021987
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
X-RAY DIFFRACTIONr_nbd_refined0.2380.3360
X-RAY DIFFRACTIONr_nbd_other0.2690.31941
X-RAY DIFFRACTIONr_nbtor_other0.0930.51070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.5181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.517
X-RAY DIFFRACTIONr_mcbond_it1.54221131
X-RAY DIFFRACTIONr_mcangle_it2.71841811
X-RAY DIFFRACTIONr_scbond_it3.4624659
X-RAY DIFFRACTIONr_scangle_it5.2676617
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1562 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.675
loose thermal2.1810
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 59 -
Rwork0.211 1183 -
obs-1183 97 %
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)
12.622-0.5-0.79613.4583-1.54923.0052-0.02390.2241-0.2117-0.19770.0408-0.03570.23690.0215-0.01690.1616-0.00070.01570.2002-0.0130.019817.071.32314.974
23.9411-0.33220.21110.9087-0.35771.92960.06790.32170.0202-0.0416-0.07730.12890.0378-0.06860.00950.17470.01010.03610.17960.00440.0075-3.50712.90114.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1181 - 118
2X-RAY DIFFRACTION2BB2 - 1182 - 118
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.8

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