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- PDB-4ahi: K40I - Angiogenin mutants and amyotrophic lateral sclerosis - a b... -

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Basic information

Entry
Database: PDB / ID: 4ahi
TitleK40I - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis
ComponentsANGIOGENIN
KeywordsHYDROLASE / AMYOTROPHIC / LATERAL SCLEROSIS / NEOVASCULARISATION
Function / homology
Function and homology information


angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation ...angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / positive regulation of phosphorylation / endocytic vesicle / RNA nuclease activity / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / peptide binding / RNA endonuclease activity / placenta development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cell migration / heparin binding / actin cytoskeleton / chromosome / ribosome binding / growth cone / actin binding / endonuclease activity / angiogenesis / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / receptor ligand activity / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / negative regulation of apoptotic process / nucleolus / signal transduction / protein homodimerization activity / extracellular space / DNA binding / extracellular region / nucleus / cytoplasm / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsThiyagarajan, N. / Ferguson, R. / Saha, S. / Pham, T. / Subramanian, V. / Acharya, K.R.
CitationJournal: Nat.Commun. / Year: 2012
Title: Structural and Molecular Insights Into the Mechanism of Action of Human Angiogenin-Als Variants in Neurons.
Authors: Thiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R.
History
DepositionFeb 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,1531
Polymers14,1531
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.204, 118.666, 37.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14153.014 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B(PLUS) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS - RIPL
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 64 TO ILE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.045
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Nov 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 4870 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 42.54 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.8 / % possible all: 39.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANG

1ang


Resolution: 2.798→27.88 Å / SU ML: 0.37 / σ(F): 0.05 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 193 4.9 %
Rwork0.2131 --
obs0.2163 3915 80.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.596 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.1786 Å20 Å20 Å2
2--19.4849 Å20 Å2
3----9.3062 Å2
Refinement stepCycle: LAST / Resolution: 2.798→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 10 958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009974
X-RAY DIFFRACTIONf_angle_d1.2791310
X-RAY DIFFRACTIONf_dihedral_angle_d16.842369
X-RAY DIFFRACTIONf_chiral_restr0.078136
X-RAY DIFFRACTIONf_plane_restr0.006174
LS refinement shellResolution: 2.7983→27.8817 Å
RfactorNum. reflection% reflection
Rfree0.2783 193 -
Rwork0.2131 3722 -
obs--80 %

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