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- PDB-1awz: 3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N N... -

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Basic information

Entry
Database: PDB / ID: 1awz
Title3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N NMR SPECTROSCOPY, 30 STRUCTURES
ComponentsANGIOGENIN
KeywordsHYDROLASE / ENDORIBONUCLEASE / ANGIOGENESIS
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 / activation of phospholipase C activity / 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 / negative regulation of smooth muscle cell proliferation / positive regulation of protein secretion / 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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsLequin, O. / Thuring, H. / Robin, M. / Lallemand, J.-Y.
CitationJournal: Eur.J.Biochem. / Year: 1997
Title: Three-dimensional solution structure of human angiogenin determined by 1H,15N-NMR spectroscopy--characterization of histidine protonation states and pKa values.
Authors: Lequin, O. / Thuring, H. / Robin, M. / Lallemand, J.Y.
History
DepositionOct 7, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANGIOGENIN


Theoretical massNumber of molelcules
Total (without water)14,1691
Polymers14,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein ANGIOGENIN /


Mass: 14169.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PANCREATIC RIBONUCLEASE SUPERFAMILY / Source: (gene. exp.) Homo sapiens (human) / Tissue: PLASMA / Plasmid: PXL694 / Species (production host): Escherichia coli / Production host: Escherichia coli B (bacteria) / Strain (production host): B
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D NOESY-HSQC
121TOCSY-HMQC
131HNHA
1412D NOESY

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Sample preparation

Sample conditionsIonic strength: 150 mM / pH: 5.0 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DIANAstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: CHARMM22 PARAMETER FILE RMS DEVIATION FROM EXPERIMENTAL DATA: NOE (A) : 0.0179 DIHEDRAL ANGLES (DEGREES) : 0.99
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 30 / Conformers submitted total number: 30

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