+Open data
-Basic information
Entry | Database: PDB / ID: 2w5l | ||||||
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Title | RNASE A-NADP COMPLEX | ||||||
Components | RIBONUCLEASE PANCREATIC | ||||||
Keywords | HYDROLASE / GLYCOPROTEIN / ENDONUCLEASE / INHIBITOR / NUCLEOTIDE / RIBONUCLEASE / ATP / ENZYME / NUCLEASE / SECRETED / GLYCATION | ||||||
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 | Chavali, G.B. / Holloway, D.E. / Baker, M.D. / Acharya, K.R. | ||||||
Citation | Journal: Biopolymers / Year: 2009 Title: Influence of Naturally-Occurring 5'-Pyrophosphate-Linked Substituents on the Binding of Adenylic Inhibitors to Ribonuclease A: An X-Ray Crystallographic Study. Authors: Holloway, D.E. / Chavali, G.B. / Leonidas, D.D. / Baker, M.D. / Acharya, K.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w5l.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w5l.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w5l_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2w5l_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2w5l_validation.xml.gz | 13 KB | Display | |
Data in CIF | 2w5l_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w5l ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5l | HTTPS FTP |
-Related structure data
Related structure data | 2w5gC 2w5iC 2w5kC 2w5mC 1afuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SIGMA CHEMICAL CO. / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | NICOTINAMI | |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 20% PEG 4000, 0.02M SODIUM CITRATE BUFFER, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 17, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 27006 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.79 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 10.3 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFU Resolution: 1.7→74.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.748 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAIN ATOMS HAVE BEEN OMITTED. RESIDUES 16-24 AND 87-90 OF EACH CHAIN HAVE POOR DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→74.33 Å
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Refine LS restraints |
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