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- PDB-7pnp: Human Angiogenin mutant-S28A -

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Basic information

Entry
Database: PDB / ID: 7pnp
TitleHuman Angiogenin mutant-S28A
ComponentsAngiogenin
KeywordsHYDROLASE / RNase5 / 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 / endocytic vesicle / RNA nuclease activity / positive regulation of phosphorylation / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / RNA endonuclease activity / peptide binding / positive regulation of protein secretion / placenta development / negative regulation of smooth muscle cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / cytoplasmic stress granule / antibacterial humoral response / cell migration / actin cytoskeleton / heparin binding / ribosome binding / actin binding / chromosome / growth cone / 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 / DNA binding / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPapaioannou, O.S.E. / Leonidas, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Biochemical Characterization of the Human Angiogenin-Proliferating Cell Nuclear Antigen Interaction.
Authors: Papaioannou, O.S.E. / Tsika, A.C. / Rovoli, M. / Papadopoulos, G.E. / Kontopidis, G. / Spyroulias, G.A. / Leonidas, D.D.
History
DepositionSep 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)14,1531
Polymers14,1531
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7060 Å2
Unit cell
Length a, b, c (Å)83.861, 37.335, 40.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14153.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli (E. coli)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Malic acid/NaOH pH 7.0, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→83.86 Å / Num. obs: 11664 / % possible obs: 93.9 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 21.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 559 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b1i

1b1i


Resolution: 1.8→41.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.015 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25424 618 5.3 %RANDOM
Rwork0.20145 ---
obs0.20431 11014 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.883 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0 Å2-0 Å2
2---4.35 Å20 Å2
3---5.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 0 58 1033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0171001
X-RAY DIFFRACTIONr_bond_other_d0.0010.019925
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.8291351
X-RAY DIFFRACTIONr_angle_other_deg1.0932.5752122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40819.69766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99615171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8991513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
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_it4.9663.592483
X-RAY DIFFRACTIONr_mcbond_other4.9423.579482
X-RAY DIFFRACTIONr_mcangle_it6.3745.357602
X-RAY DIFFRACTIONr_mcangle_other6.3775.369603
X-RAY DIFFRACTIONr_scbond_it6.4234.269518
X-RAY DIFFRACTIONr_scbond_other6.4194.279519
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0376.128750
X-RAY DIFFRACTIONr_long_range_B_refined10.94541.8071080
X-RAY DIFFRACTIONr_long_range_B_other10.96141.7291076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 43 -
Rwork0.306 651 -
obs--77.8 %

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