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Yorodumi- PDB-1afl: RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE 2'-PHOSPHATE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1afl | ||||||
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Title | RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE 2'-PHOSPHATE AT 1.7 ANGSTROM RESOLUTION | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Leonidas, D.D. / Acharya, K.R. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution. Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1afl.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1afl.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 1afl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1afl_validation.pdf.gz | 539.3 KB | Display | wwPDB validaton report |
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Full document | 1afl_full_validation.pdf.gz | 548.5 KB | Display | |
Data in XML | 1afl_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1afl_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afl ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.5748, -0.8172, 0.0419), Vector: |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #3: Chemical | #4: 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: 2.2 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED FROM 10% PEG 4000, 10 MM SODIUM CITRATE, PH 5.5 AND THEN SOAKED WITH 10 MM 5-DIPHOSPHOADENOSINE 2'- PHOSPHATE FOR 3 HRS AT 16 C, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 25897 / % possible obs: 93.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8.8 / Rsym value: 0.112 / % possible all: 89.2 |
Reflection | *PLUS Num. measured all: 87383 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 89.2 % |
-Processing
Software |
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Refinement | Resolution: 1.7→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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