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- PDB-3zbw: Crystal Structure of murine Angiogenin-3 -

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Basic information

Entry
Database: PDB / ID: 3zbw
TitleCrystal Structure of murine Angiogenin-3
ComponentsANGIOGENIN-3
KeywordsHYDROLASE / RIBONUCLEASE A
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / cell differentiation / defense response to Gram-positive bacterium ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / cell differentiation / defense response to Gram-positive bacterium / innate immune response / nucleolus / DNA binding / extracellular space / metal ion binding
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
ACETIC ACID / Angiogenin-3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsIyer, S. / Holloway, D.E. / Acharya, K.R.
CitationJournal: FEBS J. / Year: 2013
Title: Crystal Structures of Murine Angiogenin-2 and -3 - Probing 'Structure - Function' Relationships Amongst Angiogenin Homologues.
Authors: Iyer, S. / Holloway, D.E. / Acharya, K.R.
History
DepositionNov 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANGIOGENIN-3
B: ANGIOGENIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7177
Polymers28,3342
Non-polymers3835
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-110.6 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.196, 95.673, 41.669
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANGIOGENIN-3 / ANGIOGENIN-RELATED PROTEIN 2 / EF-5


Mass: 14167.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS -RIPL
References: UniProt: P97802, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 37.6 % / Description: NONE
Crystal growpH: 4.6
Details: 25% PEG 3350, 20MM SODIUM CITRATE; PH 4.6 AND 2% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 18, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 15155 / % possible obs: 75.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 23.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BWK

2bwk


Resolution: 1.801→27.679 Å / SU ML: 0.44 / σ(F): 1.39 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 792 5.2 %
Rwork0.165 --
obs0.1681 15134 75.41 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.957 Å2 / ksol: 0.448 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.8179 Å20 Å2-0.7401 Å2
2---0.4998 Å20 Å2
3---1.3177 Å2
Refinement stepCycle: LAST / Resolution: 1.801→27.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 16 222 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082048
X-RAY DIFFRACTIONf_angle_d1.1192768
X-RAY DIFFRACTIONf_dihedral_angle_d13.763757
X-RAY DIFFRACTIONf_chiral_restr0.075276
X-RAY DIFFRACTIONf_plane_restr0.005365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8009-1.91380.3622420.2353791X-RAY DIFFRACTION25
1.9138-2.06150.246900.19181547X-RAY DIFFRACTION50
2.0615-2.26880.22761330.17642483X-RAY DIFFRACTION78
2.2688-2.59690.25921780.17633155X-RAY DIFFRACTION100
2.5969-3.2710.23641830.16723151X-RAY DIFFRACTION100
3.271-27.68190.19241660.14743215X-RAY DIFFRACTION100

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