[English] 日本語
Yorodumi
- PDB-3d5g: Structure of ribonuclease Sa2 complexes with mononucleotides: new... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d5g
TitleStructure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition
ComponentsRibonuclease
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


: / RNA endonuclease activity / RNA binding
Similarity search - Function
Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBauerova-Hlinkova, V. / Dvorsky, R. / Povazanec, F. / Sevcik, J.
CitationJournal: Febs J. / Year: 2009
Title: Structure of RNase Sa2 complexes with mononucleotides - new aspects of catalytic reaction and substrate recognition
Authors: Bauerova-Hlinkova, V. / Dvorsky, R. / Perecko, D. / Povazanec, F. / Sevcik, J.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8234
Polymers32,7273
Non-polymers961
Water9,098505
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0052
Polymers10,9091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)10,9091
Polymers10,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)10,9091
Polymers10,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.655, 67.667, 57.085
Angle α, β, γ (deg.)90.00, 100.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-168-

HOH

21A-197-

HOH

-
Components

#1: Protein Ribonuclease / / ribonuclease Sa2


Mass: 10909.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: R8/26 / Plasmid: pEH200 / Production host: Escherichia coli (E. coli) / Strain (production host): NovaBlue / References: UniProt: Q53752, EC: 3.1.4.8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 30% ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000
RadiationMonochromator: monochromator SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→12 Å / Num. all: 34199 / Num. obs: 34199 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 32.16
Reflection shellResolution: 1.8→1.82 Å / Rmerge(I) obs: 0.24 / % possible all: 74.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PYL

1pyl


Resolution: 1.8→11.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.78 / SU ML: 0.083 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.203 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24323 1713 5 %RANDOM
Rwork0.17366 ---
obs0.1771 32393 97.45 %-
all-32393 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.318 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.25 Å2
2--1.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 5 505 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222377
X-RAY DIFFRACTIONr_bond_other_d0.0020.021648
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9553238
X-RAY DIFFRACTIONr_angle_other_deg1.5543.0033959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46423.203128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11715354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_nbd_refined0.2310.2637
X-RAY DIFFRACTIONr_nbd_other0.2310.21922
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21136
X-RAY DIFFRACTIONr_nbtor_other0.0920.21287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2391
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2031.51783
X-RAY DIFFRACTIONr_mcbond_other0.7771.5578
X-RAY DIFFRACTIONr_mcangle_it2.73922331
X-RAY DIFFRACTIONr_scbond_it3.68431114
X-RAY DIFFRACTIONr_scangle_it4.9544.5907
X-RAY DIFFRACTIONr_rigid_bond_restr2.61834959
X-RAY DIFFRACTIONr_sphericity_free9.9823505
X-RAY DIFFRACTIONr_sphericity_bonded4.31533960
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 114 -
Rwork0.166 1956 -
obs-852 80.95 %

+
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