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Yorodumi- PDB-5o5o: X-ray crystal structure of RapZ from Escherichia coli (P32 space ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o5o | ||||||||||||
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Title | X-ray crystal structure of RapZ from Escherichia coli (P32 space group) | ||||||||||||
Components | RNase adapter protein RapZ | ||||||||||||
Keywords | CHAPERONE / RNA binding Amino-sugar metabolism Kinase like domain PFK like domain | ||||||||||||
Function / homology | Function and homology information RNA destabilization / carbohydrate derivative binding / protein homotetramerization / molecular adaptor activity / GTP binding / protein-containing complex / RNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.404 Å | ||||||||||||
Authors | Gonzalez, G.M. / Durica-Mitic, S. / Hardwick, S.W. / Moncrieffe, M. / Resch, M. / Neumann, P. / Ficner, R. / Gorke, B. / Luisi, B.F. | ||||||||||||
Funding support | United Kingdom, Austria, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism. Authors: Gonzalez, G.M. / Durica-Mitic, S. / Hardwick, S.W. / Moncrieffe, M.C. / Resch, M. / Neumann, P. / Ficner, R. / Gorke, B. / Luisi, B.F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o5o.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5o.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o5o_validation.pdf.gz | 472.2 KB | Display | wwPDB validaton report |
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Full document | 5o5o_full_validation.pdf.gz | 490 KB | Display | |
Data in XML | 5o5o_validation.xml.gz | 39 KB | Display | |
Data in CIF | 5o5o_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5o ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5o | HTTPS FTP |
-Related 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: 32538.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rapZ, yhbJ, b3205, JW3172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0A894 #2: Chemical | ChemComp-SO4 / #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: 3.17 Å3/Da / Density % sol: 61.25 % / Description: Hexagonal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M MES, 1.1 M ammonium sulfate, 0.01 M beta-mercaptoethanol, 1 percent glycerol, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→46.33 Å / Num. obs: 20540 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 71.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.4→3.48 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.695 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.404→46.33 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.404→46.33 Å
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Refine LS restraints |
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LS refinement shell |
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