[English] 日本語
Yorodumi
- PDB-6qmn: Crystal structure of a Ribonuclease A-Onconase chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qmn
TitleCrystal structure of a Ribonuclease A-Onconase chimera
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / pancreatic ribonuclease A / alpha/beta fold / chimera
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / nucleic acid binding / lyase activity / extracellular region
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
PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBison bison (American bison)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsEsposito, L. / Vitagliano, L. / Ruggiero, A. / Picone, D. / Leone, S. / Donnarumma, F.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera.
Authors: Esposito, L. / Donnarumma, F. / Ruggiero, A. / Leone, S. / Vitagliano, L. / Picone, D.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
C: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7586
Polymers40,4733
Non-polymers2853
Water2,774154
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5862
Polymers13,4911
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.442, 51.796, 66.093
Angle α, β, γ (deg.)90.000, 93.010, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13491.060 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bison bison (American bison) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61824, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.100 M Bis-Tris pH 6.5, 28 % W/V Polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.31→28 Å / Num. obs: 16885 / % possible obs: 96.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.2
Reflection shellResolution: 2.31→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1664 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kf4

1kf4


Resolution: 2.31→27.85 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.029 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.303
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 844 5 %RANDOM
Rwork0.2046 ---
obs0.2092 16037 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.21 Å2 / Biso mean: 46.698 Å2 / Biso min: 23.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å2-0 Å22.28 Å2
2---2.54 Å20 Å2
3---4.88 Å2
Refinement stepCycle: final / Resolution: 2.31→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 15 154 2947
Biso mean--63.45 49.43 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182456
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.653962
X-RAY DIFFRACTIONr_angle_other_deg1.281.5785780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9685385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57324.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71615499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4111511
X-RAY DIFFRACTIONr_chiral_restr0.0630.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
LS refinement shellResolution: 2.309→2.369 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 60 -
Rwork0.253 1146 -
all-1206 -
obs--92.13 %

+
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