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- PDB-3plw: Ref protein from P1 bacteriophage -

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Basic information

Entry
Database: PDB / ID: 3plw
TitleRef protein from P1 bacteriophage
ComponentsRecombination enhancement function protein
KeywordsHYDROLASE / HNH nuclease / DNase
Function / homology
Function and homology information


DNA recombination / DNA repair
Similarity search - Function
Herpes Virus-1 - #190 / Recombination enhancement, RecA-dependent nuclease / : / Recombination enhancement, RecA-dependent nuclease / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Recombination enhancement function protein
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsKeck, J.L. / Lu, D. / Cox, M.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Creating Directed Double-strand Breaks with the Ref Protein: A NOVEL RecA-DEPENDENT NUCLEASE FROM BACTERIOPHAGE P1.
Authors: Gruenig, M.C. / Lu, D. / Won, S.J. / Dulberger, C.L. / Manlick, A.J. / Keck, J.L. / Cox, M.M.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Recombination enhancement function protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6024
Polymers21,3751
Non-polymers2273
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.733, 71.733, 54.236
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Recombination enhancement function protein


Mass: 21374.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: ref / Production host: Escherichia coli (E. coli) / References: UniProt: P35926
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.88 Å3/Da / Density % sol: 34.73 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium nitrate, 20% PEG3350, 0.01 M Tris-HCl, pH 8.0, 100 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionRedundancy: 13.1 % / Av σ(I) over netI: 29.26 / Number: 401946 / Rmerge(I) obs: 0.086 / Χ2: 1.22 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 30636 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.85098.810.0481.11213.6
3.023.899.810.0511.10314.5
2.633.0299.610.061.31514.7
2.392.6399.510.0731.52414.9
2.222.3999.210.0851.65214.9
2.092.2299.410.0911.54215
1.992.0998.410.1121.46615
1.91.999910.1331.38415
1.831.998.810.1551.31215
1.761.8398.610.1851.2115
1.711.7698.310.2261.11815
1.661.719810.2511.0414.8
1.621.6697.910.2880.99214.3
1.581.629810.3460.9513.5
1.541.5897.910.3650.95812.5
1.511.5497.510.3770.96610.9
1.481.519610.430.9699.4
1.451.4890.410.4460.9727.8
1.421.4581.710.4450.9646.7
1.41.4269.410.4350.9415.6
ReflectionResolution: 1.4→50 Å / Num. all: 31956 / Num. obs: 30636 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.086 / Χ2: 1.215 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.425.60.43510940.94169.4
1.42-1.456.70.44512720.96481.7
1.45-1.487.80.44614320.97290.4
1.48-1.519.40.4315040.96996
1.51-1.5410.90.37715470.96697.5
1.54-1.5812.50.36515490.95897.9
1.58-1.6213.50.34615460.9598
1.62-1.6614.30.28815620.99297.9
1.66-1.7114.80.25115521.0498
1.71-1.76150.22615501.11898.3
1.76-1.83150.18515841.2198.6
1.83-1.9150.15515441.31298.8
1.9-1.99150.13315971.38499
1.99-2.09150.11215751.46698.4
2.09-2.22150.09115761.54299.4
2.22-2.3914.90.08515961.65299.2
2.39-2.6314.90.07316011.52499.5
2.63-3.0214.70.0616181.31599.6
3.02-3.814.50.05116341.10399.8
3.8-5013.60.04817031.11298.8

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Phasing

Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.63 / Reflection: 29914 / Reflection acentric: 27632 / Reflection centric: 2282
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4-500.930.950.8314581152306
2.5-40.90.920.842903799491
2-2.50.80.810.6852994868431
1.8-20.670.680.5352444895349
1.5-1.80.520.530.4491228628494
1.4-1.50.430.430.3945014290211

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
RESOLVE2.15phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.684 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1717 1556 5.1 %RANDOM
Rwork0.1633 ---
obs0.1637 30628 95.9 %-
all-31940 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.88 Å2 / Biso mean: 15.6966 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 7 126 986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9531316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27322.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.447158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021741
X-RAY DIFFRACTIONr_mcbond_it0.661.5581
X-RAY DIFFRACTIONr_mcangle_it1.2442943
X-RAY DIFFRACTIONr_scbond_it2.123379
X-RAY DIFFRACTIONr_scangle_it3.6624.5362
LS refinement shellResolution: 1.402→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 84 -
Rwork0.279 1608 -
all-1692 -
obs--72.9 %

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