+Open data
-Basic information
Entry | Database: PDB / ID: 8amv | |||||||||||||||||||||||||||
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Title | RepB pMV158 hexamer | |||||||||||||||||||||||||||
Components | Replication protein RepB | |||||||||||||||||||||||||||
Keywords | REPLICATION / 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 | |||||||||||||||||||||||||||
Biological species | Streptococcus agalactiae (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | |||||||||||||||||||||||||||
Authors | Machon, C. / Amodio, J. / Boer, R.D. / Ruiz-Maso, J.A. / del Solar, G. / Coll, M. | |||||||||||||||||||||||||||
Funding support | Spain, 8items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8amv.cif.gz | 297.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8amv.ent.gz | 197.9 KB | Display | PDB format |
PDBx/mmJSON format | 8amv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8amv ftp://data.pdbj.org/pub/pdb/validation_reports/am/8amv | HTTPS FTP |
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-Related structure data
Related structure data | 8amtC 8amuC 3dkxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.23 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.77→45.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.097 / Num. unique obs: 3702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→45.48 Å
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Refine LS restraints |
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LS refinement shell |
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