[English] 日本語
Yorodumi
- PDB-3plw: Ref protein from P1 bacteriophage -

+
Open data


ID or keywords:

Loading...

-
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


enzyme activator activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more