[English] 日本語
Yorodumi
- PDB-1rge: HYDROLASE, GUANYLORIBONUCLEASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rge
TitleHYDROLASE, GUANYLORIBONUCLEASE
ComponentsRIBONUCLEASE
KeywordsHYDROLASE (GUANYLORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-2'-MONOPHOSPHATE / Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 Å
AuthorsSevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Ribonuclease from Streptomyces aureofaciens at atomic resolution.
Authors: Sevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7A Resolution
Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S.
#2: Journal: Eur.J.Biochem. / Year: 1993
Title: Complex of Ribonuclease Sa with a Cyclic Nucleotide and a Proposed Model for the Reaction Intermediate
Authors: Sevcik, J. / Zegers, I. / Wyns, L. / Dauter, Z. / Wilson, K.S.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution
Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G.
#4: Journal: Trends Biochem.Sci. / Year: 1990
Title: Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity
Authors: Sevcik, J. / Sanishvili, R.G. / Pavlovsky, A.G. / Polyakov, K.M.
#5: Journal: FEBS Lett. / Year: 1986
Title: Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens
Authors: Shlyapnikov, S.V. / Both, V. / Kulikov, V.A. / Dementiev, A.A. / Sevcik, J. / Zelinka, J.
#6: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification
Authors: Bacova, M. / Zelinkova, E. / Zelinka, J.
#7: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity
Authors: Zelinkova, E. / Bacova, M. / Zelinka, J.
History
DepositionJun 5, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_entry_details.has_protein_modification / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6244
Polymers21,1652
Non-polymers4592
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.730, 78.560, 38.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97076, 0.23453, 0.05116), (-0.04091, 0.37164, -0.92748), (-0.23653, 0.89827, 0.37036)
Vector: -33.23187, 21.02109, 19.04894)

-
Components

#1: Protein RIBONUCLEASE


Mass: 10582.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces aureofaciens (bacteria) / References: UniProt: P05798, EC: 3.1.27.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS DESCRIBED IN V.S.LAMZIN,Z.DAUTER,V.O.POPOV,E.H.HARUTYUNYAN,K.S.WILSON J.MOL.BIOL. (1994) V.236, 759-785.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growpH: 6.7 / Details: ROOM TEMPERATURE, PH 6.7, AMMONIUM SULFATE / Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 %protein1drop
20.1 Mphosphate1drop
322 %satammonium sulfate1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 1.15 Å / Num. obs: 62845 / % possible obs: 87.3 % / Num. measured all: 445145 / Biso Wilson estimate: 11.2 Å2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementResolution: 1.15→10 Å / Num. parameters: 18013 / Num. restraintsaints: 21102 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOU RECORDS CONTAIN ANISOTROPIC DISPLACEMENT PARAMETERS U11 U22 U33 U23 U13 U12 (ANGSTROMS**2) MULTIPLIED BY 10000. ISOTROPIC EQUIVALENTS OF ANISOTROPIC TEMPERATURE FACTORS ARE ALSO PRESENTED IN THIS ENTRY.
RfactorNum. reflection% reflection
all0.109 62714 -
obs--88 %
Solvent computationSolvent model: BASED ON BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 13 / Occupancy sum non hydrogen: 1957
Refinement stepCycle: LAST / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 29 447 1966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.304
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.16
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.3
X-RAY DIFFRACTIONs_similar_adp_cmpnt1.8
X-RAY DIFFRACTIONs_approx_iso_adps6.1
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_plane_restr0.3040.285
X-RAY DIFFRACTIONs_chiral_restr0.0850.2

+
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