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- PDB-6prk: X-ray Crystal Structure of Bacillus subtilis RicA in complex with RicF -
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Open data
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Basic information
Entry | Database: PDB / ID: 6prk | |||||||||
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Title | X-ray Crystal Structure of Bacillus subtilis RicA in complex with RicF | |||||||||
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![]() | METAL BINDING PROTEIN / RNA processing / biofilms / competence / sporulation | |||||||||
Function / homology | ![]() establishment of competence for transformation / sporulation resulting in formation of a cellular spore / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Khaja, F.T. / Jeffrey, P.D. / Neiditch, M.B. / Dubnau, D. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 87.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 248.7 KB | Display | ![]() |
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Full document | ![]() | 248.6 KB | Display | |
Data in XML | ![]() | 942 B | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6prhSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14399.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ylbF, BSU14990 / Production host: ![]() ![]() |
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#2: Protein | Mass: 14180.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ymcA, BSU17020 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% (vol/vol) PEG500 MME, 8% (vol/vol) MPD, 100 mM sodium nitrate, 100 mM MOPS, Sodium HEPES pH 7.3 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88557 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 6195 / % possible obs: 99.9 % / Redundancy: 9.95 % / Biso Wilson estimate: 105.49 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.085 / Rsym value: 0.08 / Net I/σ(I): 17.24 |
Reflection shell | Resolution: 3.2→3.26 Å / Num. unique obs: 312 / CC1/2: 0.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6PRH Resolution: 3.2→43.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.475
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Displacement parameters | Biso max: 232.24 Å2 / Biso mean: 144.79 Å2 / Biso min: 89.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→43.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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