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

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Basic information

Entry
Database: PDB / ID: 4lvk
TitleMobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6
Components
  • ACTTTAT oligonucleotide
  • ATAAAGTATAGTGTGpo oligonucleotide
  • Plasmid recombination enzyme
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 1.2Feb 28, 2024Group: 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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: Plasmid recombination enzyme
B: ACTTTAT oligonucleotide
C: ATAAAGTATAGTGTGpo oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3115
Polymers30,2333
Non-polymers782
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-42 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.743, 112.743, 91.660
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
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 ACTTTAT oligonucleotide


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).
#3: DNA chain ATAAAGTATAGTGTGpo oligonucleotide


Mass: 4976.263 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).

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Non-polymers , 3 types, 69 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion + seeding / pH: 4.6
Details: 22% PEG 4000, 0.2M Sodium Chloride, 0.1M Sodium Acetate pH4.6., VAPOR DIFFUSION + seeding, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.37→37 Å / Num. obs: 13543 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.2
Reflection shellResolution: 2.37→2.51 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
BESTdata collection
PHASERphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→36.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 18.27 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24987 715 5 %RANDOM
Rwork0.2007 ---
obs0.20312 13543 98.71 %-
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: 59.347 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å22.28 Å20 Å2
2--2.28 Å20 Å2
3----7.41 Å2
Refinement stepCycle: LAST / Resolution: 2.37→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 453 2 67 2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0182112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.92926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30124.2789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5811512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021463
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_it1.923.038764
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9654.549952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6742.881346
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: 2.372→2.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 51 -
Rwork0.336 914 -
obs--92.88 %
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)
11.99430.11990.26881.54530.13144.9057-0.12030.1164-0.0170.00940.09580.0140.15880.09680.02460.1234-0.03750.04560.15280.01530.2304-5.168242.3776-1.7303
217.70326.88281.343911.4868-5.53974.5664-0.1635-0.27530.45632.09110.54580.5871-1.1017-0.3255-0.38231.00560.33730.07010.8610.03140.1807-16.217148.455923.9607
34.68931.24760.23721.40.80350.66890.1166-0.5550.17250.1857-0.00580.0521-0.15580.2886-0.11080.496-0.30450.12330.3417-0.01550.2305-6.817449.233411.3517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 196
2X-RAY DIFFRACTION2B1 - 7
3X-RAY DIFFRACTION3C12 - 27

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