+
Open data
-
Basic information
Entry | Database: PDB / ID: 1b1j | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A. | ||||||
![]() | HYDROLASE ANGIOGENIN | ||||||
![]() | HYDROLASE / HYDROLASE (VASCULARIZATION) | ||||||
Function / homology | ![]() 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / rRNA transcription / : / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of phosphorylation / positive regulation of endothelial cell proliferation / RNA endonuclease activity / activation of protein kinase B activity / actin filament polymerization / response to hormone / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / peptide binding / placenta development / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / cell migration / chromosome / heparin binding / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / endonuclease activity / angiogenesis / rRNA binding / negative regulation of translation / response to hypoxia / defense response to Gram-positive bacterium / copper ion binding / innate immune response / signaling receptor binding / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leonidas, D.D. / Acharya, K.R. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 38.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 360.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 366.5 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b1eC ![]() 1b1iC ![]() 2angC ![]() 1angS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 14101.967 Da / Num. of mol.: 1 / Mutation: H13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % Description: DATA WAS 99.1 % COMPLETE FOR RESOLUTION RANGE 30.0-2.9 A | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 5493 / % possible obs: 58.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 1.3 / % possible all: 31.8 |
Reflection | *PLUS Num. measured all: 21688 |
Reflection shell | *PLUS % possible obs: 31.8 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ANG Resolution: 2→20 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.084 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.348 |