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- PDB-1un4: CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T80A -

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Basic information

Entry
Database: PDB / ID: 1un4
TitleCRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T80A
ComponentsANGIOGENIN
KeywordsHYDROLASE / RIBONUCLEASE / NUCLEASE / ENDONUCLEASE / ANGIOGENESIS / PYRROLIDONE CARBOXYLIC ACID
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 / stress granule assembly / peptide binding / RNA endonuclease activity / 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 / ribosome binding / chromosome / 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 / cytoplasm / 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
CITRIC ACID / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHolloway, D.E. / Chavali, G.B. / Acharya, K.R.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystallographic Studies on Structural Features that Determine the Enzymatic Specificity and Potency of Human Angiogenin: Thr44, Thr80 and Residues 38-41
Authors: Holloway, D.E. / Chavali, G.B. / Hares, M.C. / Baker, M.D. / Subbarao, G.V. / Shapiro, R. / Acharya, K.R.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Refined Crystal Structures of Native Human Angiogenin and Two Active Site Variants: Implications for the Unique Functional Properties of an Enzyme Involved in Neovascularisation During Tumour Growth
Authors: Leonidas, D.D. / Shapiro, R. / Allen, S.C. / Subbarao, G.V. / Veluraja, K. / Acharya, K.R.
#2: Journal: Biochemistry / Year: 1998
Title: Structural Features that Determine the Enzymatic Potency and Specificity of Human Angiogenin: Threonine-80 and Residues 58-70 and 116-123
Authors: Shapiro, R.
History
DepositionSep 4, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 6, 2004ID: 1H0E
Revision 1.0Feb 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 2023Group: 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 2.2Nov 13, 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)14,3142
Polymers14,1221
Non-polymers1921
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.549, 38.297, 39.043
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-2037-

HOH

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14121.979 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P03950, EC: 3.1.27.5
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, ALA 104 THR (RESIDUE NUMBERING BASED ON SWISSPROT SEQUENCE DATABASE) ...ENGINEERED MUTATION IN CHAIN A, ALA 104 THR (RESIDUE NUMBERING BASED ON SWISSPROT SEQUENCE DATABASE). THE RESIDUE NUMBER IN THE COORDINATES IS 80. ANGIOGENIC RIBONUCLEASE THAT BINDS TO ACTIN ON THE SURFACE OF ENDOTHELIAL CELLS
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 %
Crystal growpH: 5.2
Details: 15% PEG 4000, 0.02% DIOXANE, 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER, PH 5.2
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG40001reservoir
20.02 %(v/v)dioxane1reservoir
30.2 Msodium potassium tartrate1reservoir
40.02 Mcitric acid/NaOH1reservoirpH5.2
515-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 17, 2001 / Details: RH/SI MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 7942 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5.1 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. measured all: 36676 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B1I

1b1i


Resolution: 2.1→43.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.252 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 367 4.6 %RANDOM
Rwork0.191 ---
obs0.193 7551 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 13 54 980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.2581.9391376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02807
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.2285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.211
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.5604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4112976
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6523416
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6654.5400
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 28
Rwork0.203 535
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.26

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