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- PDB-5m9g: Human angiogenin PD variant K54R -

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Basic information

Entry
Database: PDB / ID: 5m9g
TitleHuman angiogenin PD variant K54R
ComponentsAngiogenin
KeywordsHYDROLASE / Parkinson's / RNase / angiogenesis
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 / hematopoietic stem cell proliferation / homeostatic process / 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 / peptide binding / RNA endonuclease activity / stress granule assembly / 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 / cell migration / antibacterial humoral response / actin cytoskeleton / heparin binding / chromosome / ribosome binding / actin binding / growth cone / angiogenesis / endonuclease activity / 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 / cytosol / cytoplasm
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
DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBradshaw, W.J. / Rehman, S. / Pham, T.T.K. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust083191 United Kingdom
Wellcome Trust088464 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into human angiogenin variants implicated in Parkinson's disease and Amyotrophic Lateral Sclerosis.
Authors: Bradshaw, W.J. / Rehman, S. / Pham, T.T. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
History
DepositionNov 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5843
Polymers14,3281
Non-polymers2562
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint5 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.904, 118.755, 37.053
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-317-

HOH

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Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14328.248 Da / Num. of mol.: 1 / Mutation: K54R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Na/K tartrate 0.1 M HEPES 3% propanol 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→32.5 Å / Num. obs: 8730 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.994 / Net I/σ(I): 6.7
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 842 / CC1/2: 0.904 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANG

1ang


Resolution: 2.28→32.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.589 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27057 841 9.7 %RANDOM
Rwork0.22015 ---
obs0.22506 7868 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å20 Å2-0 Å2
2--9.38 Å20 Å2
3----6.33 Å2
Refinement stepCycle: 1 / Resolution: 2.28→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 17 32 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191041
X-RAY DIFFRACTIONr_bond_other_d0.0020.02965
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9351402
X-RAY DIFFRACTIONr_angle_other_deg1.00232213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3812255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72415173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9561514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9524.535496
X-RAY DIFFRACTIONr_mcbond_other2.9524.535495
X-RAY DIFFRACTIONr_mcangle_it4.7726.794620
X-RAY DIFFRACTIONr_mcangle_other4.7696.796621
X-RAY DIFFRACTIONr_scbond_it3.3395.032545
X-RAY DIFFRACTIONr_scbond_other3.3365.032545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6627.35783
X-RAY DIFFRACTIONr_long_range_B_refined8.33152.1261089
X-RAY DIFFRACTIONr_long_range_B_other8.33652.1671088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 63 -
Rwork0.475 583 -
obs--99.85 %

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