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

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Basic information

Entry
Database: PDB / ID: 4lvm
TitleMobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (23nt). Mn-bound crystal structure at pH 6.5
Components
  • ACTTTAT oligonucleotide
  • ATAAAGTATAGTGTGT oligonucleotide
  • 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_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
E: ATAAAGTATAGTGTGT oligonucleotide
C: Plasmid recombination enzyme
D: ACTTTAT oligonucleotide
F: ATAAAGTATAGTGTGT oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,80015
Polymers60,4656
Non-polymers3349
Water25214
1
A: Plasmid recombination enzyme
B: ACTTTAT oligonucleotide
E: ATAAAGTATAGTGTGT oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3707
Polymers30,2333
Non-polymers1384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-53 kcal/mol
Surface area12860 Å2
MethodPISA
2
C: Plasmid recombination enzyme
D: ACTTTAT oligonucleotide
F: ATAAAGTATAGTGTGT oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4298
Polymers30,2333
Non-polymers1975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-69 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.340, 130.120, 87.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Plasmid recombination enzyme / Mobilization protein


Mass: 23168.918 Da / Num. of mol.: 2
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, 4 molecules BDEF

#2: DNA chain ACTTTAT oligonucleotide


Mass: 2087.409 Da / Num. of mol.: 2
Fragment: oligonucleotide_1 mimicking pMV158 oriT DNA hairpin
Source method: obtained synthetically
Details: Oligonucleotides were obtained from Biomers (Ulm, Germany).
#3: DNA chain ATAAAGTATAGTGTGT oligonucleotide


Mass: 4976.263 Da / Num. of mol.: 2
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 , 5 types, 23 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8000, 02.M MgAc(4H20), 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97243 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 3.1→28.4 Å / Num. obs: 13500 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 76.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→28.4 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.894 / SU B: 55.145 / SU ML: 0.508 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29359 732 5.1 %RANDOM
Rwork0.25486 ---
obs0.25696 13500 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 87.628 Å2
Baniso -1Baniso -2Baniso -3
1--12.83 Å20 Å20 Å2
2---5.32 Å20 Å2
3---18.15 Å2
Refinement stepCycle: LAST / Resolution: 3.1→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 864 9 14 4031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4092.215786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02124.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022920
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_it0.4441.51905
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86823056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96132274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.634.52730
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: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 46 -
Rwork0.43 974 -
obs--97.79 %
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)
11.04020.7683-0.1896-0.852-0.39412.4486-0.0051-0.2709-0.34270.49030.0411-0.39710.17210.0846-0.0360.46710.0103-0.03140.59850.01020.469840.250120.101137.7115
2-4.4771-0.7495-0.27261.06630.180.3987-0.0646-0.5184-0.09170.2946-0.0159-0.0233-0.04160.03110.08050.6772-0.0333-0.00420.7790.03280.426935.612118.172747.3371
3-1.0152-0.9899-0.04140.9454-0.43251.23220.0996-0.3403-0.31160.10520.0455-0.03640.0702-0.2085-0.14510.4483-0.00010.0730.5549-0.00990.359431.019319.18933.7666
40.05030.44650.57550.53480.18610.99970.0219-0.28920.09990.2645-0.0685-0.0687-0.0561-0.01250.04660.48040.00610.00050.596-0.05940.404934.289829.170441.3691
51.53750.19060.17360.70790.15471.6266-0.0648-0.1790.42010.03370.03570.0094-0.27110.06150.02910.4633-0.04780.010.4559-0.05130.413340.964533.561529.6552
60.06170.92050.38952.62341.57281.7177-0.2345-0.4228-0.2394-0.2946-0.02610.334-0.0146-0.41540.26070.3988-0.1257-0.0160.3778-0.01780.451623.047311.301819.0333
71.93026.7081-1.37422.55511.36342.37190.5195-0.48010.4788-0.4294-0.4645-0.5322-0.05390.1482-0.05510.4539-0.1032-0.12550.5424-0.14470.425239.296127.973624.5237
8-6.47226.58767.141633.69731.8802-7.25890.7618-0.6018-0.08392.1456-0.4981.5918-0.68780.9906-0.26370.36710.00440.05140.91880.04610.517850.055628.261135.487
90.994-0.39360.18361.1792-0.3531.0138-0.00610.0330.0675-0.0111-0.00390.0267-0.0021-0.01640.010.174-0.0252-0.00580.1939-0.00720.056234.054737.24042.414
100.5153-0.2143-0.13370.6434-0.13330.2689-0.0060.16840.1754-0.1512-0.0246-0.21020.01390.04390.03050.2375-0.00250.02680.24580.03940.071641.020638.2994-6.7685
111.46511.03870.0510.91711.19031.83070.00120.2081-0.4974-0.022-0.0210.2110.1243-0.28380.01980.38960.0077-0.03110.38610.04440.354435.641425.3366-12.2942
1211.3348-1.18494.56685.2809-2.42432.1876-0.00580.47470.3952-0.3001-0.1905-0.0678-0.38080.16760.19630.41830.12830.02810.35580.07330.448524.375359.5212-17.909
131.56351.5110.92598.41761.95371.47420.11780.34240.1036-0.1071-0.0728-0.33920.25620.2376-0.04490.31120.0341-0.00590.39950.00440.279326.23542.9927-16.0211
142.3584-2.70861.71850.06330.97713.51270.2335-0.17520.4467-0.0812-0.00160.24020.2049-0.0488-0.23190.3371-0.0388-0.02440.3365-0.01330.232733.605727.2906-12.9239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 26
2X-RAY DIFFRACTION2A33 - 65
3X-RAY DIFFRACTION3A66 - 90
4X-RAY DIFFRACTION4A91 - 150
5X-RAY DIFFRACTION5A151 - 199
6X-RAY DIFFRACTION6E12 - 18
7X-RAY DIFFRACTION7E19 - 23
8X-RAY DIFFRACTION8E24 - 27
9X-RAY DIFFRACTION9C2 - 101
10X-RAY DIFFRACTION10C102 - 170
11X-RAY DIFFRACTION11C171 - 192
12X-RAY DIFFRACTION12F12 - 16
13X-RAY DIFFRACTION13F17 - 20
14X-RAY DIFFRACTION14F21 - 25

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