+Open data
-Basic information
Entry | Database: PDB / ID: 1q9e | ||||||
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Title | RNase T1 variant with adenine specificity | ||||||
Components | Guanyl-specific ribonuclease T1 precursor | ||||||
Keywords | HYDROLASE / Ribonuclease / Adenine specificity | ||||||
Function / homology | Function and homology information hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Czaja, R. / Struhalla, M. / Hoeschler, K. / Saenger, W. / Straeter, N. / Hahn, U. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: RNase T1 Variant RV Cleaves Single-Stranded RNA after Purines Due to Specific Recognition by the Asn46 Side Chain Amide. Authors: Czaja, R. / Struhalla, M. / Saenger, W. / Hahn, U. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallography & NMR System Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / DeLano, W.L. / Gros, P. / Grosse-Kunstleve, R.W. / Jiang, J.S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q9e.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q9e.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q9e_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 1q9e_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 1q9e_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1q9e_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q9e ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q9e | HTTPS FTP |
-Related structure data
Related structure data | 1ch0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11129.745 Da / Num. of mol.: 3 / Mutation: K41E, Y42F, N43R, Y45W, E46N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: RNTA / Plasmid: pA2T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3 #2: Chemical | #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: 2.19 Å3/Da / Density % sol: 43.82 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / pH: 9 Details: PEG4000, magnesium chloride, Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 9.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8459 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 28456 / % possible obs: 90.6 % / Biso Wilson estimate: 21.4 Å2 |
Reflection shell | Resolution: 1.7→20 Å / % possible all: 95.5 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 31400 / Num. measured all: 70573 / Rmerge(I) obs: 0.037 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CH0 Resolution: 1.7→18.01 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 953216.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 50.16 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→18.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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