+Open data
-Basic information
Entry | Database: PDB / ID: 1k5b | |||||||||
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Title | Crystal Structure of Human Angiogenin Variant des(121-123) | |||||||||
Components | Angiogenin | |||||||||
Keywords | HYDROLASE / ribonuclease / vascularization | |||||||||
Function / homology | Function and homology information activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / homeostatic process ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / homeostatic process / rRNA transcription / : / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of phosphorylation / RNA endonuclease activity / actin filament polymerization / positive regulation of endothelial cell proliferation / activation of protein kinase B activity / response to hormone / placenta development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / peptide binding / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / heparin binding / chromosome / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / rRNA binding / response to hypoxia / defense response to Gram-positive bacterium / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Leonidas, D.D. / Shapiro, R. / Subbarao, G.V. / Russo, A. / Acharya, K.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystallographic studies on the role of the C-terminal segment of human angiogenin in defining enzymatic potency. Authors: Leonidas, D.D. / Shapiro, R. / Subbarao, G.V. / Russo, A. / Acharya, K.R. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Refined Crystal Structures of Native Human Angiogenin and Two Active Site Variants: Implications for the Unique Functional Properties of an Enzyme Involved in Neovascularisation During Tumour Growth Authors: Leonidas, D.D. / Shapiro, R. / Allen, S.C. / Subbarao, G.V. / Veluraja, K. / 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 | 1k5b.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5b.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1k5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5b ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5b | HTTPS FTP |
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-Related structure data
Related structure data | 1k58C 1k59C 1k5aC 2angS 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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Unit cell |
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-Components
#1: Protein | Mass: 13740.504 Da / Num. of mol.: 1 / Mutation: DEL(121-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.29 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: sodium citrate, sodium potassium tartrate, PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. all: 10158 / Num. obs: 10158 / % possible obs: 92.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 90 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 38216 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ANG Resolution: 1.8→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.304 |