[English] 日本語
Yorodumi
- PDB-7ord: The crystal structure of the domain-swapped dimer of onconase (2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ord
TitleThe crystal structure of the domain-swapped dimer of onconase (2)
ComponentsProtein P-30
KeywordsHYDROLASE / Ribonuclease / Onconase / Onconase dimer / 3D domain swapping / antitumor activity
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ACETATE ION / Protein P-30
Similarity search - Component
Biological speciesLithobates pipiens (northern leopard frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMerlino, A. / Loreto, D.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme.
Authors: Gotte, G. / Campagnari, R. / Loreto, D. / Bettin, I. / Calzetti, F. / Menegazzi, M. / Merlino, A.
History
DepositionJun 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Protein P-30
BBB: Protein P-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1034
Polymers23,9482
Non-polymers1552
Water1,74797
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-43 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.750, 28.540, 61.480
Angle α, β, γ (deg.)90.000, 94.240, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein P-30 / Onconase


Mass: 11973.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates pipiens (northern leopard frog)
Production host: Escherichia coli (E. coli)
References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5 25% PEG 3350 0.2 M Ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→58.59 Å / Num. obs: 11313 / % possible obs: 97.4 % / Redundancy: 5.9 % / CC1/2: 1 / Rrim(I) all: 0.124 / Net I/σ(I): 10.6
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11313 / CC1/2: 0.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONC

1onc


Resolution: 2.14→58.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.645 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.345 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2668 526 4.81 %
Rwork0.2118 10410 -
all0.214 --
obs-10936 94.081 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.428 Å2-0 Å20.077 Å2
2---0.043 Å2-0 Å2
3---0.455 Å2
Refinement stepCycle: LAST / Resolution: 2.14→58.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 9 97 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131726
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171555
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6542343
X-RAY DIFFRACTIONr_angle_other_deg1.2351.5823647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3535212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35923.16579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05115309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.241156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021900
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
X-RAY DIFFRACTIONr_nbd_refined0.2040.2353
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21448
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2801
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.224
X-RAY DIFFRACTIONr_nbd_other0.2480.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.220
X-RAY DIFFRACTIONr_mcbond_it2.4742.907846
X-RAY DIFFRACTIONr_mcbond_other2.4752.904845
X-RAY DIFFRACTIONr_mcangle_it3.9964.3431058
X-RAY DIFFRACTIONr_mcangle_other3.9944.3461059
X-RAY DIFFRACTIONr_scbond_it3.2483.252880
X-RAY DIFFRACTIONr_scbond_other3.2313.226875
X-RAY DIFFRACTIONr_scangle_it5.1324.7451285
X-RAY DIFFRACTIONr_scangle_other5.1284.7091279
X-RAY DIFFRACTIONr_lrange_it8.41435.1311880
X-RAY DIFFRACTIONr_lrange_other8.30535.0681872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.1960.424160.279516X-RAY DIFFRACTION60.9393
2.196-2.2560.318290.276629X-RAY DIFFRACTION80.9348
2.256-2.3210.327310.27674X-RAY DIFFRACTION88.7909
2.321-2.3920.306380.26696X-RAY DIFFRACTION94.2234
2.392-2.4710.323390.261704X-RAY DIFFRACTION98.5411
2.471-2.5570.275430.244700X-RAY DIFFRACTION100
2.557-2.6530.252340.247651X-RAY DIFFRACTION99.8542
2.653-2.7620.27320.235649X-RAY DIFFRACTION100
2.762-2.8840.368320.243636X-RAY DIFFRACTION99.7015
2.884-3.0250.256440.235576X-RAY DIFFRACTION99.839
3.025-3.1880.28300.221575X-RAY DIFFRACTION99.6705
3.188-3.3810.275240.191530X-RAY DIFFRACTION100
3.381-3.6130.277240.188521X-RAY DIFFRACTION98.3755
3.613-3.9020.252310.176458X-RAY DIFFRACTION99.1886
4.272-4.7740.237190.151416X-RAY DIFFRACTION99.5423
6.73-9.4610.299180.186241X-RAY DIFFRACTION98.855

+
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