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- PDB-1un5: ARH-II, AN ANGIOGENIN/RNASE A CHIMERA -

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Basic information

Entry
Database: PDB / ID: 1un5
TitleARH-II, AN ANGIOGENIN/RNASE A CHIMERA
ComponentsANGIOGENIN
KeywordsHYDROLASE / PANCREATIC RIBONUCLEASE / ANGIOGENESIS / ANGIOGENIN / CHIMERA / HYBRID / HOMOLOG SCANNING MUTAGENESIS
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 / pancreatic ribonuclease / ribonuclease A activity / 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 / nucleic acid binding / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / lyase activity / 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 / Ribonuclease pancreatic / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHolloway, D.E. / Baker, M.D. / 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: 1990
Title: Mutagenesis of Residues Flanking Lys-40 Enhances the Enzymatic Activity and Reduces the Angiogenic Potency of Angiogenin
Authors: Harper, J.W. / Fox, E.A. / Shapiro, R. / Vallee, B.L.
History
DepositionSep 4, 2003Deposition site: PDBE / Processing site: PDBE
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 1.3Dec 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 1.4Nov 6, 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)14,6502
Polymers14,4571
Non-polymers1921
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.270, 123.973, 37.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14457.428 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 38-42 IN THE COORDINATES ARE FROM BOVINE PANCREATIC RIBONUCLEASE A
Source: (gene. exp.) HOMO SAPIENS (human) / Description: GUEST SEGMENT IS BOVINE. SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P03950, UniProt: P00656, 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.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREPLACEMENT OF ANGIOGENIN 62-65 WITH RIBONUCLEASE A 64-68. (RESIDUE NUMBERING BASED ON SWISSPROT ...REPLACEMENT OF ANGIOGENIN 62-65 WITH RIBONUCLEASE A 64-68. (RESIDUE NUMBERING BASED ON SWISSPROT SEQUENCE DATABASE). THE RESIDUE NUMBERS REPLACED IN THE COORDINATES ARE 38-41 OF ANGIOGENIN WITH RESIDUES 38-42 OF BOVINE RIBONUCLEASE. 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 5.4
Details: 10% PEG 6000, PH 5.4 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG60001reservoir
20.2 Msodium potassium tartrate1reservoir
30.02 Mcitric acid/NaOH1reservoirpH5.4
415-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 4, 2002 / Details: RH/SI MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 5767 / % possible obs: 95.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.1
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 8.3 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. measured all: 35002 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 8.3

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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 2ANG

2ang


Resolution: 2.6→67.42 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.954 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 259 4.5 %RANDOM
Rwork0.207 ---
obs0.208 5503 95.1 %-
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: 52.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--4.13 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 13 9 945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.3421.9361395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975122
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_restr0.0950.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02811
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8351.5613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.562992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7513421
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9824.5403
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: 2.6→2.69 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.235 27
Rwork0.126 546
Refinement
*PLUS
Highest resolution: 2.6 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_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.34

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