[English] 日本語
Yorodumi
- PDB-4lvl: MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lvl
TitleMobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Thiophosphate). Mn-bound crystal structure at pH 6.8
Components
  • DNA (5'-D(*AP*CP*TP*TP*TP*AP*T)-3')
  • DNA (5'-D(*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*GP*TP*GP*TP*GP*(TS6))-3')
  • Plasmid recombination enzyme
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / Pfam Family: Mob_Pre (PF01076). MOB Relaxase Family: MOBv / relaxase/endonuclease / oriT DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA recombination / DNA binding
Similarity search - Function
Plasmid recombination enzyme / Plasmid recombination enzyme / BirA Bifunctional Protein; domain 2 - #30 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Plasmid recombination enzyme
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPluta, R. / Boer, D.R. / Coll, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance.
Authors: Pluta, R. / Boer, D.R. / Lorenzo-Diaz, F. / Russi, S. / Gomez, H. / Fernandez-Lopez, C. / Perez-Luque, R. / Orozco, M. / Espinosa, M. / Coll, M.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasmid recombination enzyme
B: DNA (5'-D(*AP*CP*TP*TP*TP*AP*T)-3')
C: DNA (5'-D(*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*GP*TP*GP*TP*GP*(TS6))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1867
Polymers30,0243
Non-polymers1614
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-54 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.420, 112.420, 90.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Plasmid recombination enzyme / Mobilization protein


Mass: 23168.918 Da / Num. of mol.: 1
Fragment: Relaxase Domain of MobM protein, UNP residues 2-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: pre, mob / Plasmid: pQE-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P13925

-
DNA chain , 2 types, 2 molecules BC

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


Mass: 2087.409 Da / Num. of mol.: 1
Fragment: oligonucleotide_1 mimicking pMV158 oriT DNA hairpin
Source method: obtained synthetically
Details: Oligonucleotides were obtained from Biomers (Ulm, Germany).
Source: (synth.) Synthetic DNA (others)
#3: DNA chain DNA (5'-D(*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*GP*TP*GP*TP*GP*(TS6))-3')


Mass: 4768.116 Da / Num. of mol.: 1
Fragment: oligonucleotide_2 mimicking pMV158 oriT DNA hairpin
Source method: obtained synthetically
Details: Oligonucleotides were obtained from Biomers (Ulm, Germany).
Source: (synth.) Synthetic DNA (others)

-
Non-polymers , 3 types, 161 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, seeding / pH: 6.8
Details: 22% PEG 6000, 0.3M sodium cloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, seeding, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→41.1 Å / Num. obs: 16824 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.32 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
BESTdata collection
PHASERphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.559 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23739 865 4.9 %RANDOM
Rwork0.18652 ---
obs0.18904 16822 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 449 8 157 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0172237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.7433102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25124.54599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3981512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021594
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_it0.7891.544822
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2932.3121039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1691.6061414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 53 -
Rwork0.275 1236 -
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)
11.14581.75270.23372.8102-0.26125.0033-0.06820.10050.0396-0.05570.0844-0.0336-0.0140.5061-0.01620.0227-0.0077-0.060.0856-0.00610.179310.743-46.0153-1.6326
26.574111.1481-1.216720.8599-7.64716.52440.0147-0.01890.31630.1764-0.09960.5069-0.36030.62230.08490.5001-0.0040.09740.5468-0.04580.634319.825-48.5769-14.4987
34.524-0.0996-0.59670.314-0.68849.13140.16530.68240.0071-0.1496-0.1995-0.1416-0.50230.26160.03420.17120.10150.07930.1950.08710.110.8428-40.2665-14.3241
43.5120.81541.8981.7570.49725.0245-0.12910.02280.07850.06420.0761-0.1959-0.61890.66520.0530.0878-0.0869-0.01150.1093-0.00880.077714.4475-37.52686.1115
51.98240.21350.84241.07980.01037.1377-0.04670.03350.12090.076-0.01220.1048-0.4208-0.33730.05890.03090.0189-0.00170.0194-0.00340.06432.2642-38.82-1.8004
64.0917-2.22870.05063.46560.79664.70970.12640.2934-0.5202-0.2075-0.21870.41050.4389-0.72040.09220.0706-0.0516-0.00520.1791-0.00630.1147-4.2096-49.9414-0.779
710.88094.4884-0.36679.38721.12934.2080.026-0.4268-0.70690.8259-0.2224-0.22490.26130.22880.19640.1399-0.0059-0.02740.15850.0130.089616.2756-48.121923.7921
85.70430.94146.46824.83743.329113.8020.0157-0.81180.09470.440.0596-0.1326-0.2947-0.858-0.07540.1028-0.0092-0.0230.21410.00630.086113.8704-44.500724.4133
95.5798-2.4287-1.95811.10930.49585.9428-0.0183-0.1429-0.1296-0.03470.0641-0.01750.882-0.1927-0.04580.1858-0.0813-0.05580.06310.01930.23771.0943-52.8250.4823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 26
2X-RAY DIFFRACTION2A27 - 31
3X-RAY DIFFRACTION3A32 - 50
4X-RAY DIFFRACTION4A51 - 89
5X-RAY DIFFRACTION5A90 - 156
6X-RAY DIFFRACTION6A157 - 197
7X-RAY DIFFRACTION7B1 - 7
8X-RAY DIFFRACTION8C12 - 18
9X-RAY DIFFRACTION9C19 - 26

+
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