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- PDB-1k5b: Crystal Structure of Human Angiogenin Variant des(121-123) -

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Basic information

Entry
Database: PDB / ID: 1k5b
TitleCrystal Structure of Human Angiogenin Variant des(121-123)
ComponentsAngiogenin
KeywordsHYDROLASE / ribonuclease / vascularization
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 / chromosome / ribosome binding / 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: 1.8 Å
AuthorsLeonidas, D.D. / Shapiro, R. / Subbarao, G.V. / Russo, A. / Acharya, K.R.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystallographic studies on the role of the C-terminal segment of human angiogenin in defining enzymatic potency.
Authors: Leonidas, D.D. / Shapiro, R. / Subbarao, G.V. / Russo, A. / 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.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Refinement description
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / software / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 30, 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)13,9332
Polymers13,7411
Non-polymers1921
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.450, 40.410, 32.980
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


Mass: 13740.504 Da / Num. of mol.: 1 / Mutation: DEL(121-123)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#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.: 57 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: sodium citrate, sodium potassium tartrate, PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1dropin water
20.2 Msodium potassium tartrate1reservoir
320 mMsodium citrate1reservoirpH5.2
410-15 %(w/v)PEG60001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODESIEMENS11.5418
SYNCHROTRONSRS PX9.520.8
Detector
TypeIDDetectorDate
XENTRONICS1AREA DETECTORFeb 11, 1997
MARRESEARCH2IMAGE PLATE
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.81
ReflectionResolution: 1.8→30 Å / Num. all: 10158 / Num. obs: 10158 / % possible obs: 92.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / % possible all: 90
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 38216
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
X-GENdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANG

2ang


Resolution: 1.8→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 528 5.3 %RANDOM
Rwork0.206 ---
all0.206 9945 --
obs0.206 9945 88.4 %-
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 13 57 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.281.5
X-RAY DIFFRACTIONx_mcangle_it3.612
X-RAY DIFFRACTIONx_scbond_it3.752
X-RAY DIFFRACTIONx_scangle_it5.62.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 85 5.1 %
Rwork0.304 1585 -
obs-1585 91.2 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor obs: 0.304

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