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- PDB-4ahm: V113I - Angiogenin mutants and amyotrophic lateral sclerosis - a ... -

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Basic information

Entry
Database: PDB / ID: 4ahm
TitleV113I - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis
ComponentsANGIOGENIN
KeywordsHYDROLASE / ANG / ALS / NEOVASCULARISATION
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 / activation of protein kinase B activity / RNA endonuclease 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 / antibacterial humoral response / heparin binding / chromosome / actin binding / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / response to hypoxia / rRNA binding / 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
L(+)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3332
Polymers14,1831
Non-polymers1501
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.269, 118.284, 37.215
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-2025-

HOH

21A-2072-

HOH

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14183.062 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 137 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: 3.3 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 13478 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 7.1 / % possible all: 69

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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: 1.96→29.571 Å / SU ML: 0.2 / σ(F): 0.08 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1100 9.2 %
Rwork0.1957 --
obs0.1982 12013 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.692 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.053 Å20 Å20 Å2
2--19.6176 Å20 Å2
3----14.5646 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 10 99 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007998
X-RAY DIFFRACTIONf_angle_d1.0531341
X-RAY DIFFRACTIONf_dihedral_angle_d14.708379
X-RAY DIFFRACTIONf_chiral_restr0.073139
X-RAY DIFFRACTIONf_plane_restr0.005179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.04920.2037930.1918981X-RAY DIFFRACTION66
2.0492-2.15720.23181210.18941184X-RAY DIFFRACTION79
2.1572-2.29240.23181370.20021334X-RAY DIFFRACTION89
2.2924-2.46930.24811320.1961453X-RAY DIFFRACTION95
2.4693-2.71760.2231590.20911455X-RAY DIFFRACTION97
2.7176-3.11050.22751370.20531495X-RAY DIFFRACTION97
3.1105-3.91740.2051510.17641495X-RAY DIFFRACTION97
3.9174-29.57440.20391700.19341516X-RAY DIFFRACTION94

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