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- PDB-5m9r: Human angiogenin ALS variant F100I -

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Basic information

Entry
Database: PDB / ID: 5m9r
TitleHuman angiogenin ALS variant F100I
ComponentsAngiogenin
KeywordsHYDROLASE / ALS / 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 / L(+)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 2, 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 23, 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
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2397
Polymers28,5322
Non-polymers7065
Water4,252236
1
A: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6734
Polymers14,2661
Non-polymers4063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5663
Polymers14,2661
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.878, 34.781, 52.920
Angle α, β, γ (deg.)89.72, 84.17, 84.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14266.217 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Na/K tartrate 0.1 M Na cacodylate 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.44→52.7 Å / Num. obs: 37557 / % possible obs: 95.1 % / Redundancy: 2.4 % / CC1/2: 0.989 / Net I/σ(I): 6.5
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1635 / CC1/2: 0.937 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANG

1ang


Resolution: 1.44→52.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.153 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19544 1768 4.7 %RANDOM
Rwork0.17232 ---
obs0.17341 35788 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.679 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20.13 Å20.44 Å2
2---0.13 Å2-0.54 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.44→52.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 47 236 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192094
X-RAY DIFFRACTIONr_bond_other_d0.0020.021936
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9422839
X-RAY DIFFRACTIONr_angle_other_deg1.01934463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57222.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3351524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
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_it1.0081.092990
X-RAY DIFFRACTIONr_mcbond_other1.0051.091989
X-RAY DIFFRACTIONr_mcangle_it1.6851.6371239
X-RAY DIFFRACTIONr_mcangle_other1.6851.6381240
X-RAY DIFFRACTIONr_scbond_it1.2951.2741104
X-RAY DIFFRACTIONr_scbond_other1.2951.2741104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0891.8431591
X-RAY DIFFRACTIONr_long_range_B_refined4.55614.8932446
X-RAY DIFFRACTIONr_long_range_B_other4.36114.092353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 123 -
Rwork0.182 2365 -
obs--83.63 %

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