[English] 日本語
Yorodumi
- PDB-5eop: Crystal structure of human Angiogenin at 1.35 Angstroms resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eop
TitleCrystal structure of human Angiogenin at 1.35 Angstroms resolution
ComponentsAngiogenin
KeywordsHYDROLASE
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 / endocytic vesicle / RNA nuclease activity / positive regulation of phosphorylation / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / RNA endonuclease activity / peptide binding / positive regulation of protein secretion / placenta development / negative regulation of smooth muscle cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / cytoplasmic stress granule / antibacterial humoral response / cell migration / actin cytoskeleton / heparin binding / ribosome binding / actin binding / chromosome / growth cone / endonuclease activity / angiogenesis / 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 / DNA binding / extracellular space / extracellular region / nucleus / cytosol / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsChatzileontiadou, D.S.M. / Tsirkone, V.G. / Dossi, K. / Leonidas, D.D.
CitationJournal: Febs Lett. / Year: 2016
Title: The ammonium sulfate inhibition of human angiogenin.
Authors: Chatzileontiadou, D.S. / Tsirkone, V.G. / Dossi, K. / Kassouni, A.G. / Liggri, P.G. / Kantsadi, A.L. / Stravodimos, G.A. / Balatsos, N.A. / Skamnaki, V.T. / Leonidas, D.D.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiogenin


Theoretical massNumber of molelcules
Total (without water)13,9441
Polymers13,9441
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.664, 37.559, 33.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

-
Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 13943.792 Da / Num. of mol.: 1 / Fragment: UNP residues 26-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: Malic acid/NaOH pH 7.0 PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0403 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2015
RadiationMonochromator: monochromator crystals Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 1.35→42.83 Å / Num. obs: 23977 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B1I

1b1i


Resolution: 1.35→42.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.871 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19155 1222 5.1 %RANDOM
Rwork0.1474 ---
obs0.14968 22728 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.35→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 125 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191038
X-RAY DIFFRACTIONr_bond_other_d0.0020.02969
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.921410
X-RAY DIFFRACTIONr_angle_other_deg1.12432229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.10922.22254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69715179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7591513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02274
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7681.501501
X-RAY DIFFRACTIONr_mcbond_other1.7571.493500
X-RAY DIFFRACTIONr_mcangle_it2.3982.248630
X-RAY DIFFRACTIONr_mcangle_other2.3982.255631
X-RAY DIFFRACTIONr_scbond_it2.1871.914537
X-RAY DIFFRACTIONr_scbond_other2.1851.919538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7252.72777
X-RAY DIFFRACTIONr_long_range_B_refined4.07320.9451248
X-RAY DIFFRACTIONr_long_range_B_other3.69219.891202
X-RAY DIFFRACTIONr_rigid_bond_restr2.32732007
X-RAY DIFFRACTIONr_sphericity_free32.367542
X-RAY DIFFRACTIONr_sphericity_bonded9.78152058
LS refinement shellResolution: 1.347→1.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 81 -
Rwork0.168 1587 -
obs--94.5 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more