+Open data
-Basic information
Entry | Database: PDB / ID: 1dza | ||||||
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Title | 3-D structure of a HP-RNase | ||||||
Components | RIBONUCLEASE 1 | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / RNASE / HUMAN PANCREATIC RIBONUCLEASE | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Pous, J. / Canals, A. / Terzyan, S.S. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Three-Dimensional Structure of a Human Pancreatic Ribonuclease Variant, a Step Forward in the Design of Cytotoxic Ribonucleases Authors: Pous, J. / Canals, A. / Terzyan, S.S. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dza.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dza.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dza_validation.pdf.gz | 369.5 KB | Display | wwPDB validaton report |
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Full document | 1dza_full_validation.pdf.gz | 374.5 KB | Display | |
Data in XML | 1dza_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1dza_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dza ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dza | HTTPS FTP |
-Related structure data
Related structure data | 7rsaS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 14572.326 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: 100A FORMILMETHIONINE (FME) / Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Gene: PM7 / Organ: PANCREAS / Plasmid: PM7 / Gene (production host): PM7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07998, EC: 3.1.27.5 #2: Water | ChemComp-HOH / | Compound details | MUTATIONS: R104A, K106A, Q109E, D116G, S117N, P150S; | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.8 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8342 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8342 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.9 Å / Num. obs: 25881 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.826 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.111 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.255 / % possible all: 63.2 |
Reflection | *PLUS Num. measured all: 80829 |
Reflection shell | *PLUS % possible obs: 63.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RSA Resolution: 1.65→19.9 Å / SU B: 2.13159 / SU ML: 0.07304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11915 / ESU R Free: 0.12127
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Displacement parameters | Biso mean: 21.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.9 Å
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Refine LS restraints |
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