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- PDB-8amu: RepB pMV158 OBD domain bound to DDR region -

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Basic information

Entry
Database: PDB / ID: 8amu
TitleRepB pMV158 OBD domain bound to DDR region
Components
  • DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')
  • Replication protein RepB
KeywordsREPLICATION / rolling circle replication / RepB / pMV158 / DDR region
Function / homology
Function and homology information


DNA topoisomerase activity / extrachromosomal circular DNA / DNA replication / DNA binding / identical protein binding
Similarity search - Function
Plasmid replication protein / Plasmid replication protein, C-terminal domain superfamily / Plasmid replication protein, origin binding domain
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Replication protein RepB
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAmodio, J. / Machon, C. / Boer, R.D. / Ruiz-Maso, J.A. / del Solar, G. / Coll, M.
Funding support Spain, 8items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)RYC-2011-09071 Spain
Ministry of Economy and Competitiveness (MINECO)BFU2014-53550-P Spain
Ministry of Economy and Competitiveness (MINECO)BFU2017-83720-P Spain
Ministry of Economy and Competitiveness (MINECO)MDM-2014-0435 Spain
Ministry of Economy and Competitiveness (MINECO)SEV-2015-0500 Spain
Ministry of Economy and Competitiveness (MINECO)RTI2018-097114-B-I00 Spain
Ministry of Economy and Competitiveness (MINECO)BFU2010-19597 Spain
Ministry of Economy and Competitiveness (MINECO)8-CSD00C-08-41920 Spain
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein.
Authors: Machon, C. / Ruiz-Maso, J.A. / Amodio, J. / Boer, D.R. / Bordanaba-Ruiseco, L. / Bury, K. / Konieczny, I. / Del Solar, G. / Coll, M.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 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: Replication protein RepB
B: Replication protein RepB
C: DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')
D: DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')
E: Replication protein RepB
F: Replication protein RepB
G: DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')
H: DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,06211
Polymers93,8978
Non-polymers1653
Water46826
1
A: Replication protein RepB
B: Replication protein RepB
C: DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')
D: DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0586
Polymers46,9494
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Replication protein RepB
F: Replication protein RepB
G: DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')
H: DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0035
Polymers46,9494
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.234, 33.619, 289.672
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "E"
d_4ens_1(chain "F" and resid 2 through 132)
d_1ens_2chain "C"
d_2ens_2chain "G"
d_1ens_3chain "D"
d_2ens_3chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAVALA1 - 131
d_21ens_1ALAVALB1 - 131
d_31ens_1ALAVALE1 - 131
d_41ens_1ALAVALF2 - 132
d_11ens_2DTDTC
d_21ens_2DTDTG
d_11ens_3DADAD
d_21ens_3DADAH

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.963295073656, 0.0324012194793, 0.266482198367), (-0.0308964061095, 0.999474168241, -0.00983865378721), (-0.266660857944, 0.00124418450295, 0.963789623749)-20.5996497627, 18.8272598288, -16.502523427
2given(0.999915706393, 0.00353622869335, 0.012493005823), (0.00346226382695, -0.999976381048, 0.00593717734094), (0.0125137059681, -0.0058934227927, -0.999904332789)7.62551374622, -165.615882183, 143.436582685
3given(0.891146126075, 0.0317526197811, 0.452603969402), (0.0338093876887, -0.999422006766, 0.00354650472932), (0.452454978187, 0.0121418091203, -0.891704586276)-36.3159087885, -183.688684362, 147.277876876
4given(0.991337757553, -0.0211905820374, 0.129616394343), (-0.0234209325459, -0.999602294056, 0.0157071205626), (0.129232002105, -0.0186067985048, -0.991439799827)-9.06555934802, -165.812003586, 136.366437818
5given(0.988807551342, -0.00219855982891, 0.149180403348), (-0.00538507567079, -0.999765821075, 0.0209595794429), (0.149099387552, -0.0215283381868, -0.988587832864)-9.14812080021, -167.074022031, 135.090549868

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Components

#1: Protein
Replication protein RepB


Mass: 16413.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: repB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13921
#2: DNA chain DNA (5'-D(*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*TP*CP*GP*GP*CP*GP*AP*CP*TP*TP*TP*T)-3')


Mass: 7029.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus agalactiae (bacteria)
#3: DNA chain DNA (5'-D(*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*AP*AP*AP*AP*GP*TP*CP*GP*CP*CP*GP*A)-3')


Mass: 7092.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus agalactiae (bacteria)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM Tris-HCl pH 8.0 50 mM MgCl2 23 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.99→24.7 Å / Num. obs: 17954 / % possible obs: 90.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 69.78 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 3.7
Reflection shellResolution: 2.99→24.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1433

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Processing

Software
NameVersionClassification
REFMAC1.20rc4_4425refinement
PHENIX1.20rc4_4425refinement
autoPROCdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKX

3dkx


Resolution: 3→24.69 Å / SU ML: 0.5133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.6769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2818 921 5.13 %
Rwork0.227 17033 -
obs0.2298 17954 90.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71 Å2
Refinement stepCycle: LAST / Resolution: 3→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 1874 3 26 6196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416485
X-RAY DIFFRACTIONf_angle_d1.81449142
X-RAY DIFFRACTIONf_chiral_restr0.08871029
X-RAY DIFFRACTIONf_plane_restr0.0123814
X-RAY DIFFRACTIONf_dihedral_angle_d29.34451477
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.13763951823
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.926891268924
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.03271481157
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.999465806008
ens_3d_2DX-RAY DIFFRACTIONTorsion NCS1.07429717873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.150.4183990.33491876X-RAY DIFFRACTION71.61
3.15-3.350.32691070.30682346X-RAY DIFFRACTION86.65
3.35-3.610.33311300.27782500X-RAY DIFFRACTION95.29
3.61-3.970.35261430.24592539X-RAY DIFFRACTION95.31
3.97-4.540.2441560.20142528X-RAY DIFFRACTION95.18
4.54-5.710.22581340.19472583X-RAY DIFFRACTION95.23
5.71-24.690.25891520.1972661X-RAY DIFFRACTION94.21

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