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- PDB-4ktw: Lactococcus phage 67 RuvC - apo form -

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Basic information

Entry
Database: PDB / ID: 4ktw
TitleLactococcus phage 67 RuvC - apo form
ComponentsRuvC endonuclease
KeywordsHYDROLASE / endonuclease / DNA junctions / replication / recombination / phage packaging / Holliday junction / RNase-H fold / DNA junction endonuclease / Holliday junctions and other 2- & 3-way DNA junctions
Function / homology
Function and homology information


nucleic acid binding / metal ion binding
Similarity search - Function
Lactococcus phage 712, M3 / Lactococcus phage M3 protein / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLactococcus phage bIL67 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.68 Å
AuthorsRafferty, J.B. / Green, V.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Mutants of phage bIL67 RuvC with enhanced Holliday junction binding selectivity and resolution symmetry.
Authors: Green, V. / Curtis, F.A. / Sedelnikova, S. / Rafferty, J.B. / Sharples, G.J.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: RuvC endonuclease
B: RuvC endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3994
Polymers36,2452
Non-polymers1542
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-15 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 66.900, 73.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RuvC endonuclease


Mass: 18122.617 Da / Num. of mol.: 2 / Mutation: D8N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage bIL67 (virus) / Gene: orf23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q38242
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% w/v PEG3350, 0.1 M KCl, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856, 0.9785, 0.9787
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2007
RadiationMonochromator: unknown / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.97851
30.97871
ReflectionResolution: 1.68→33.5 Å / Num. all: 35135 / Num. obs: 35135 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.3 % / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.68→33.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.735 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23714 1895 5.2 %RANDOM
Rwork0.19697 ---
obs0.19912 34637 99.82 %-
all-27422 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.68→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 10 299 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9443419
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1895319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65724.513113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60915434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5781510
X-RAY DIFFRACTIONr_chiral_restr0.140.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3951.51574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36722508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.473961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5574.5910
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 153 -
Rwork0.295 2504 -
obs--99.63 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
10.629518.90231.6925
25.619722.8411-27.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 160
2X-RAY DIFFRACTION2B2 - 160

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