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Yorodumi- PDB-5xgt: Crystal structure of the N-terminal domain of Staphylococcus aure... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xgt | ||||||
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Title | Crystal structure of the N-terminal domain of Staphylococcus aureus single-stranded DNA-binding protein SsbA at 1.82 angstrom resolution | ||||||
Components | Single-stranded DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / single-strand DNA binding protein / SsbA | ||||||
Function / homology | Function and homology information nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Huang, Y.H. / Chen, C.J. / Huang, C.Y. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase. Authors: Huang, Y.H. / Guan, H.H. / Chen, C.J. / Huang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xgt.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xgt.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xgt_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 5xgt_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 5xgt_validation.xml.gz | 11 KB | Display | |
Data in CIF | 5xgt_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xgt ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xgt | HTTPS FTP |
-Related structure data
Related structure data | 1x3eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12645.094 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: ED98 Gene: ssb_1, A7U48_3558, AS852_01830, BJI72_0272, EDCC5055_00340, QU38_04380 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1JHQ1, UniProt: A0A0H3JNP6*PLUS #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 4000, 100mM HEPES sodium salt pH 7.5, 100mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→30 Å / Num. obs: 23485 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 27.47 |
Reflection shell | Resolution: 1.82→1.9 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X3E Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.812 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.221 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→30 Å
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Refine LS restraints |
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