+Open data
-Basic information
Entry | Database: PDB / ID: 7w05 | ||||||
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Title | 12 mutant Ribonuclease from Hericium erinaceus GMP binding form | ||||||
Components | Ribonuclease T1 | ||||||
Keywords | DNA BINDING PROTEIN / catalytic activity enzyme anti tumor activity nucleic acid binding RNA binding | ||||||
Function / homology | : / Ribonuclease/ribotoxin / RNA nuclease activity / RNA binding / metal ion binding / GUANOSINE / DI(HYDROXYETHYL)ETHER / Ribonuclease T1 Function and homology information | ||||||
Biological species | Hericium erinaceus (bearded tooth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Takebe, K. / Chida, T. / Suzuki, M. / Itagaki, T. / Morita, Y. / Uzawa, N. / Kobayashi, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: 12 mutant Ribonuclease from Hericium erinaceus GMP binding form Authors: Takebe, K. / Chida, T. / Suzuki, M. / Uzawa, N. / Kobayashi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w05.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w05.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 7w05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w05_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7w05_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7w05_validation.xml.gz | 8 KB | Display | |
Data in CIF | 7w05_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/7w05 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/7w05 | HTTPS FTP |
-Related structure data
Related structure data | 6ls1S S: Starting model for refinement |
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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: 10703.474 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hericium erinaceus (bearded tooth) / Gene: RNHe1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1Q4V2 |
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#2: Chemical | ChemComp-GMP / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→46.31 Å / Num. obs: 22027 / % possible obs: 98.77 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 33.78 |
Reflection shell | Resolution: 1.19→1.21 Å / Num. unique obs: 1444 / CC1/2: 0.821 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LS1 Resolution: 1.29→11.9947 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.79 Å2 / Biso mean: 15.4588 Å2 / Biso min: 6.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.29→11.9947 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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