[English] 日本語
Yorodumi
- PDB-1t2h: Y81W mutant of RNase Sa from Streptomyces aureofaciens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t2h
TitleY81W mutant of RNase Sa from Streptomyces aureofaciens
ComponentsGuanyl-specific ribonuclease Sa
KeywordsHYDROLASE / mutant / ribonuclease
Function / homology
Function and homology information


ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
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
Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsSevcik, J. / Urbanikova, L.
CitationJournal: Biophys.J. / Year: 2004
Title: Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease sa.
Authors: Alston, R.W. / Urbanikova, L. / Sevcik, J. / Lasagna, M. / Reinhart, G.D. / Scholtz, J.M. / Pace, C.N.
History
DepositionApr 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanyl-specific ribonuclease Sa
B: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3073
Polymers21,2112
Non-polymers961
Water10,611589
1
A: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7022
Polymers10,6061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanyl-specific ribonuclease Sa


Theoretical massNumber of molelcules
Total (without water)10,6061
Polymers10,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.206, 64.309, 77.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Guanyl-specific ribonuclease Sa / RNase Sa


Mass: 10605.527 Da / Num. of mol.: 2 / Mutation: Y81W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: BMK / Gene: U39467 / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): NOVABLUE / References: UniProt: P05798, EC: 3.1.27.3
#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.: 589 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.812 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003
RadiationMonochromator: Si(111) double monochromator system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1→33.3 Å / Num. obs: 103514 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 34.5
Reflection shellResolution: 1→1.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 10.2 / Num. unique all: 4121 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rgg

1rgg


Resolution: 1→33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.31 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16593 5166 5 %RANDOM
Rwork0.14524 ---
obs0.14631 98348 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.056 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 5 589 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211739
X-RAY DIFFRACTIONr_bond_other_d0.0030.021448
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9392386
X-RAY DIFFRACTIONr_angle_other_deg0.87433374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785214
X-RAY DIFFRACTIONr_chiral_restr0.0910.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021998
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02372
X-RAY DIFFRACTIONr_nbd_refined0.2330.2393
X-RAY DIFFRACTIONr_nbd_other0.2630.21775
X-RAY DIFFRACTIONr_nbtor_other0.0830.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2471
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.293
X-RAY DIFFRACTIONr_mcbond_it1.1791.51068
X-RAY DIFFRACTIONr_mcangle_it1.80421743
X-RAY DIFFRACTIONr_scbond_it2.0683671
X-RAY DIFFRACTIONr_scangle_it2.9124.5643
X-RAY DIFFRACTIONr_rigid_bond_restr0.93221739
X-RAY DIFFRACTIONr_sphericity_free5.7665589
X-RAY DIFFRACTIONr_sphericity_bonded4.16651691
LS refinement shellResolution: 1→1.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 367 -
Rwork0.166 7157 -
obs-4121 97.7 %

+
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