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- PDB-2bwk: Murine angiogenin, sulphate complex -

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Basic information

Entry
Database: PDB / ID: 2bwk
TitleMurine angiogenin, sulphate complex
ComponentsANGIOGENIN
KeywordsHYDROLASE / RIBONUCLEASE / ANGIOGENESIS / CANCER
Function / homology
Function and homology information


tRNA destabilization / angiogenin-PRI complex / negative regulation of translation in response to stress / Adherens junctions interactions / tRNA-specific ribonuclease activity / signaling / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / cellular response to osmotic stress / hematopoietic stem cell proliferation / rRNA transcription ...tRNA destabilization / angiogenin-PRI complex / negative regulation of translation in response to stress / Adherens junctions interactions / tRNA-specific ribonuclease activity / signaling / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / cellular response to osmotic stress / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / negative regulation of cellular senescence / endocytic vesicle / RNA nuclease activity / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / central nervous system development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / heparin binding / actin binding / growth cone / endonuclease activity / angiogenesis / response to hypoxia / copper ion binding / signaling receptor binding / neuronal cell body / negative regulation of apoptotic process / nucleolus / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular region / nucleus / 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
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHolloway, D.E. / Chavali, G.B. / Hares, M.C. / Subramanian, V. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Murine Angiogenin: Features of the Substrate- and Cell-Binding Regions and Prospects for Inhibitor-Binding Studies.
Authors: Holloway, D.E. / Chavali, G.B. / Hares, M.C. / Subramanian, V. / Acharya, K.R.
History
DepositionJul 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: 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 ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9853
Polymers13,7931
Non-polymers1922
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.762, 56.266, 35.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE


Mass: 13792.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Plasmid: PMANG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P21570, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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 %
Crystal growpH: 4.5 / Details: 25% PEG 4000, 0.2M (NH4)2SO4, UNBUFFERED, pH 4.50

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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: Sep 20, 1999
RadiationMonochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 20302 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5 / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGI

1agi


Resolution: 1.5→42.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.817 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1039 5.1 %RANDOM
Rwork0.178 ---
obs0.179 19236 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 10 108 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9291331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1721.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6611511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02754
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2340
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2658
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8062607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6823961
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0044.5422
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8636370
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.196 73
Rwork0.177 1169

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