+Open data
-Basic information
Entry | Database: PDB / ID: 6prh | |||||||||
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Title | X-ray Crystal Structure of Bacillus subtilis RicA | |||||||||
Components | RicA | |||||||||
Keywords | METAL BINDING PROTEIN / RNA processing / biofilms / competence / sporulation | |||||||||
Function / homology | Function and homology information Biofilm formation YmcA / : / YheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||
Authors | Tarique, F.K. / Neiditch, M.B. / Dubnau, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mbio / Year: 2019 Title: Structure-Function Studies of the Bacillus subtilis Ric Proteins Identify the Fe-S Cluster-Ligating Residues and Their Roles in Development and RNA Processing. Authors: Adusei-Danso, F. / Khaja, F.T. / DeSantis, M. / Jeffrey, P.D. / Dubnau, E. / Demeler, B. / Neiditch, M.B. / Dubnau, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6prh.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6prh.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 6prh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/6prh ftp://data.pdbj.org/pub/pdb/validation_reports/pr/6prh | HTTPS FTP |
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-Related structure data
Related structure data | 6prkC 2pihS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14180.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: ymcA, BSU17020 / Production host: Escherichia coli (E. coli) / References: UniProt: O31779 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.75 Å3/Da / Density % sol: 55.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.0, 150 mM NaCl, 65% (vol/vol) MPD |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→50 Å / Num. obs: 9208 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.055 / Rrim(I) all: 0.151 / Χ2: 2.028 / Net I/av σ(I): 15.06 / Net I/σ(I): 10.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PIH Resolution: 2.08→29.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.027 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.163 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 95.71 Å2 / Biso mean: 36.796 Å2 / Biso min: 20.07 Å2
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Refinement step | Cycle: final / Resolution: 2.08→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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