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- PDB-5m9m: Human angiogenin PD variant Q77P -

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Basic information

Entry
Database: PDB / ID: 5m9m
TitleHuman angiogenin PD variant Q77P
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 / 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 / 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 / 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 / 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
TRIETHYLENE GLYCOL / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiogenin
B: Angiogenin
C: Angiogenin
D: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,98723
Polymers57,0774
Non-polymers1,91119
Water5,945330
1
A: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9457
Polymers14,2691
Non-polymers6766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4613
Polymers14,2691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7787
Polymers14,2691
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8046
Polymers14,2691
Non-polymers5345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.170, 50.337, 62.190
Angle α, β, γ (deg.)103.42, 103.59, 110.40
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14269.219 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 349 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350

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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: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→56.8 Å / Num. obs: 60548 / % possible obs: 96.6 % / Redundancy: 14.8 % / CC1/2: 0.988 / Net I/σ(I): 7.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2326 / CC1/2: 0.622 / % possible all: 70.4

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Processing

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

1ang


Resolution: 1.65→56.75 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 2.987 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27046 2002 3.3 %RANDOM
Rwork0.23167 ---
obs0.23296 58537 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å21.27 Å2-0.16 Å2
2--0.51 Å20.19 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.65→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 107 330 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194155
X-RAY DIFFRACTIONr_bond_other_d0.0020.023877
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9475620
X-RAY DIFFRACTIONr_angle_other_deg0.97138922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71421.875208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0581552
X-RAY DIFFRACTIONr_chiral_restr0.0890.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021065
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_it1.4632.0791953
X-RAY DIFFRACTIONr_mcbond_other1.4632.0791952
X-RAY DIFFRACTIONr_mcangle_it2.3653.112444
X-RAY DIFFRACTIONr_mcangle_other2.3653.1112445
X-RAY DIFFRACTIONr_scbond_it1.6922.4062202
X-RAY DIFFRACTIONr_scbond_other1.6912.4062202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6673.5053161
X-RAY DIFFRACTIONr_long_range_B_refined5.51424.784493
X-RAY DIFFRACTIONr_long_range_B_other5.49624.5684444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 108 -
Rwork0.305 3281 -
obs--72.6 %

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