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- PDB-1ang: CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN REVEALS THE STRUCTURAL BASI... -

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Basic information

Entry
Database: PDB / ID: 1ang
TitleCRYSTAL STRUCTURE OF HUMAN ANGIOGENIN REVEALS THE STRUCTURAL BASIS FOR ITS FUNCTIONAL DIVERGENCE FROM RIBONUCLEASE
ComponentsANGIOGENIN
KeywordsHYDROLASE (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 / 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 / positive regulation of phosphorylation / ovarian follicle development / 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 / cell migration / actin cytoskeleton / chromosome / heparin binding / actin binding / growth cone / antibacterial humoral response / cytoplasmic vesicle / angiogenesis / endonuclease activity / 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
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)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsAcharya, K.R. / Allen, S. / Shapiro, R. / Riordan, J.F. / Vallee, B.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease.
Authors: Acharya, K.R. / Shapiro, R. / Allen, S.C. / Riordan, J.F. / Vallee, B.L.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Analysis of Human Angiogenin
Authors: Acharya, K.R. / Subramamian, V. / Shapiro, R. / Riordan, J.F. / Vallee, B.L.
History
DepositionJan 18, 1994Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
Water00
1
A: ANGIOGENIN

A: ANGIOGENIN


Theoretical massNumber of molelcules
Total (without water)28,3382
Polymers28,3382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)83.400, 120.600, 37.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: SER 37 - PRO 38 OMEGA = 96.94 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 91

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Components

#1: Protein ANGIOGENIN


Mass: 14169.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P03950

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.01 Msodium citrate1drop
30.2 Msodium potassium tartrate1reservoir
420-25 %PEG60001reservoir
50.5 %beta-octyl glucoside1reservoir
60.01 Msodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 7229 / % possible obs: 88 % / Observed criterion σ(F): 0 / Num. measured all: 41725 / Rmerge(I) obs: 0.11

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.22 -
obs0.22 6609
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 0 0 993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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