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Yorodumi- PDB-1afk: CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1afk | ||||||
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Title | CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE-3'-PHOSPHATE | ||||||
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 / MOLECULAR REPLACEMENT / 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 | 1afk.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1afk.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1afk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1afk_validation.pdf.gz | 523.1 KB | Display | wwPDB validaton report |
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Full document | 1afk_full_validation.pdf.gz | 526.2 KB | Display | |
Data in XML | 1afk_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1afk_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afk ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afk | HTTPS FTP |
-Related structure data
Related structure data | 1aflC 1afuC 3rn3S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: (-0.59498, -0.803215, 0.029055), 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: 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 20% PEG 4000, 20 MM SODIUM CITRATE, PH 5.5 AND THEN SOAKED WITH 1MM 5' DIPHOSPHOADENOSINE 3'-PHOSPHATE FOR 2.5 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: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 24687 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.7→1.77 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.339 / % possible all: 82.4 |
Reflection | *PLUS Num. measured all: 73892 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RN3 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 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Displacement parameters | Biso mean: 22.3 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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