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- PDB-8amv: RepB pMV158 hexamer -

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Basic information

Entry
Database: PDB / ID: 8amv
TitleRepB pMV158 hexamer
ComponentsReplication protein RepB
KeywordsREPLICATION / rolling circle replication / RepB / pMV158
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 / Replication Protein E1; Chain: A, - #30 / Plasmid replication protein / Plasmid replication protein, C-terminal domain superfamily / Plasmid replication protein, origin binding domain / Replication Protein E1; Chain: A, / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Replication protein RepB
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsMachon, C. / Amodio, J. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Replication protein RepB
D: Replication protein RepB
E: Replication protein RepB
F: Replication protein RepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,31513
Polymers145,7236
Non-polymers5937
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-93 kcal/mol
Surface area60930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.910, 79.330, 114.900
Angle α, β, γ (deg.)90.000, 104.924, 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-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 4 - 203 / Label seq-ID: 4 - 203

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB
33(chain 'C' and resid 4 through 203)CC
44(chain 'E' and resid 4 through 203)EE
55chain 'F'FF

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Components

#1: Protein
Replication protein RepB


Mass: 24287.105 Da / Num. of mol.: 6
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Na/K phosphate pH 6.2 200 mM NaCl 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.77→45.52 Å / Num. obs: 40217 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 76.65 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.8
Reflection shellResolution: 2.77→45.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.097 / Num. unique obs: 3702

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKX

3dkx


Resolution: 2.77→45.48 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 1976 4.92 %
Rwork0.2182 38195 -
obs0.2206 40171 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.93 Å2
Refinement stepCycle: LAST / Resolution: 2.77→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9533 0 31 51 9615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119738
X-RAY DIFFRACTIONf_angle_d1.410313139
X-RAY DIFFRACTIONf_chiral_restr0.07431502
X-RAY DIFFRACTIONf_plane_restr0.00971620
X-RAY DIFFRACTIONf_dihedral_angle_d5.74391272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.840.35081380.34812479X-RAY DIFFRACTION90.62
2.84-2.920.37941450.3232691X-RAY DIFFRACTION99.96
2.92-30.31571570.29192724X-RAY DIFFRACTION99.86
3-3.10.31861320.26612754X-RAY DIFFRACTION99.93
3.1-3.210.30161390.23952718X-RAY DIFFRACTION99.97
3.21-3.340.32261520.2592718X-RAY DIFFRACTION99.9
3.34-3.490.30731430.2372745X-RAY DIFFRACTION99.93
3.49-3.670.28951420.21942735X-RAY DIFFRACTION100
3.67-3.90.29151220.21082744X-RAY DIFFRACTION99.97
3.9-4.20.30631470.21262738X-RAY DIFFRACTION99.9
4.21-4.630.22451510.18842744X-RAY DIFFRACTION99.83
4.63-5.30.26241190.19912791X-RAY DIFFRACTION99.97
5.3-6.670.24991450.21922776X-RAY DIFFRACTION99.97
6.67-45.480.20771440.19332838X-RAY DIFFRACTION99.6

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