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- PDB-4lvl: MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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)

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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


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.75 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

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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

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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

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