+Open data
-Basic information
Entry | Database: PDB / ID: 8amt | |||||||||||||||||||||||||||
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Title | OBD-RepB pMV158 domain | |||||||||||||||||||||||||||
Components | Replication protein RepBDNA replication | |||||||||||||||||||||||||||
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: 1.5 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 | 8amt.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8amt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8amt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8amt ftp://data.pdbj.org/pub/pdb/validation_reports/am/8amt | HTTPS FTP |
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-Related structure data
Related structure data | 8amuC 8amvC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15327.007 Da / Num. of mol.: 1 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 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MN / | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tri-sodium citrate pH 5.0 1M LiCl 30 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→32.66 Å / Num. obs: 26009 / % possible obs: 99.8 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.5→32.66 Å / Rmerge(I) obs: 1.387 / Num. unique obs: 1268 / Rpim(I) all: 0.023 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DKX Resolution: 1.5→32.682 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.16 / SU B: 1.041 / SU ML: 0.039 / Average fsc free: 0.9548 / Average fsc work: 0.9605 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.062 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.903 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→32.682 Å
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Refine LS restraints |
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LS refinement shell |
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