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- PDB-4qfj: The crystal structure of rat angiogenin-heparin complex -

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Entry
Database: PDB / ID: 4qfj
TitleThe crystal structure of rat angiogenin-heparin complex
ComponentsAngiogenin
KeywordsHYDROLASE / catalytic / angiogenesis
Function / homology
Function and homology information


tRNA destabilization / tRNA-specific ribonuclease activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / response to yeast / antifungal humoral response / rRNA transcription / activation of phospholipase C activity / basement membrane ...tRNA destabilization / tRNA-specific ribonuclease activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / response to yeast / antifungal humoral response / rRNA transcription / activation of phospholipase C activity / basement membrane / RNA nuclease activity / positive regulation of phosphorylation / actin filament polymerization / positive regulation of endothelial cell proliferation / response to hormone / liver development / negative regulation of smooth muscle cell proliferation / positive regulation of protein secretion / peptide binding / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / actin binding / antibacterial humoral response / growth cone / angiogenesis / endonuclease activity / nucleic acid binding / response to hypoxia / defense response to Gram-positive bacterium / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / nucleolus / protein homodimerization activity / extracellular space / nucleus
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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsYeo, K.J. / Hwang, E. / Min, K.M. / Hwang, K.Y. / Jeon, Y.H. / Chang, S.I. / Cheong, H.K.
CitationJournal: To be Published
Title: The crystal structure of rat angiogenin-heparin complex
Authors: Yeo, K.J. / Hwang, E. / Min, K.M. / Hwang, K.Y. / Jeon, Y.H. / Chang, S.I. / Cheong, H.K.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_chem_comp_identifier.comp_id / _pdbx_chem_comp_identifier.identifier / _pdbx_chem_comp_identifier.program / _pdbx_chem_comp_identifier.type / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.atom_id_1 / _pdbx_entity_branch_link.atom_id_2 / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_link.leaving_atom_id_1 / _pdbx_entity_branch_link.leaving_atom_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiogenin
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0877
Polymers28,0862
Non-polymers2,0015
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-75 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.415, 42.420, 154.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Angiogenin /


Mass: 14042.957 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 24-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ang, Ang1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5WRG2
#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1750.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9% PEG8000, 5mM zinc acetate, 100mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. obs: 13833 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 2.196→2.24 Å / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWK

2bwk


Resolution: 2.196→38.189 Å / SU ML: 0.63 / σ(F): 1.35 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1397 10.14 %
Rwork0.2141 --
obs0.2195 13781 99.18 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.091 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.9639 Å2-0 Å2-0 Å2
2---2.3663 Å20 Å2
3----4.5976 Å2
Refinement stepCycle: LAST / Resolution: 2.196→38.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 115 68 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011920
X-RAY DIFFRACTIONf_angle_d1.3342599
X-RAY DIFFRACTIONf_dihedral_angle_d14.654737
X-RAY DIFFRACTIONf_chiral_restr0.078285
X-RAY DIFFRACTIONf_plane_restr0.005326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.196-2.27440.29131280.2236119398
2.2744-2.36550.33871400.22471223100
2.3655-2.47310.28911340.22821239100
2.4731-2.60340.27491390.21411209100
2.6034-2.76650.32141330.23481240100
2.7665-2.980.31511470.23421226100
2.98-3.27980.26961420.23321253100
3.2798-3.7540.20971400.1958123299
3.754-4.72830.22541470.1688126599
4.7283-38.19470.27831470.2414130496

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