[English] 日本語
Yorodumi
- PDB-1b2m: THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b2m
TitleTHREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
Components
  • 5'-R(*GP*(U34))-3'
  • RIBONUCLEASE T1
KeywordsHYDROLASE/RNA / HYDROLASE / ENDORIBONUCLEASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArni, R.K. / Watanabe, L. / Ward, R.J. / Kreitman, R.J. / Kumar, K. / Walz Jr., F.G.
Citation
Journal: Biochemistry / Year: 1999
Title: Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.
Authors: Arni, R.K. / Watanabe, L. / Ward, R.J. / Kreitman, R.J. / Kumar, K. / Walz Jr., F.G.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites
Authors: Arni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Metcalf Jr., P.F.G.W.
#2: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
Authors: Kostrewa, D. / Choe, H.-W. / Heinemann, U. / Saenger, W.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, V. / Maslowska, M. / Tokuoka, R. / Saenger, W.
#5: Journal: Fresenius Z.Anal.Chem. / Year: 1987
Title: Structure and Function of the Enzyme Ribonuclease T1
Authors: Arni, R. / Heinemann, U. / Saenger, W.
#6: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallization of Ribonuclease T1
Authors: Martin, P.O. / Tulinsky, A. / Walz, F.G.
History
DepositionNov 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 9, 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-R(*GP*(U34))-3'
D: 5'-R(*GP*(U34))-3'
E: 5'-R(*GP*(U34))-3'
A: RIBONUCLEASE T1
B: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)24,0495
Polymers24,0495
Non-polymers00
Water1,65792
1
C: 5'-R(*GP*(U34))-3'
A: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)11,7142
Polymers11,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-R(*GP*(U34))-3'
E: 5'-R(*GP*(U34))-3'
B: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)12,3353
Polymers12,3353
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.910, 90.290, 33.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0701, 0.9676, -0.2427), (-0.5247, 0.1711, 0.8339), (0.8484, 0.1858, 0.4957)51.299, 4.649, -14.759
2given(0.5413, 0.6404, 0.5469), (0.0409, 0.6272, -0.7778), (-0.8398, 0.4433, 0.3133)-16.614, 43.666, 67.113

-
Components

#1: RNA chain 5'-R(*GP*(U34))-3'


Mass: 620.441 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Protein RIBONUCLEASE T1 /


Mass: 11093.644 Da / Num. of mol.: 2 / Mutation: GLN 25 VARIANT / Source method: isolated from a natural source / Details: RNASE T1 COMPLEXED WITH 5'-R(*GP*(CH2)U)-3 / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growpH: 4.1 / Details: pH 4.10
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2TRIS11
3MGCL211
4PEG 400011
5PEG 400012
Crystal grow
*PLUS
pH: 4.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMsodium acetate1drop
210 mg/mlprotein1drop
30.1 MTris-HCl1reservoir
40.2 M1reservoirMgCl2
530 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 11298 / % possible obs: 75 % / Observed criterion σ(I): 2 / Rsym value: 0.64
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 75 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RNT

1rnt


Resolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10 %RANDOM
Rwork0.187 ---
obs0.187 9879 75 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 120 0 92 1774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 26734
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42

+
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