[English] 日本語
Yorodumi
- PDB-4g6s: Minimal Hairpin Ribozyme in the Transition State with A38P Variation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g6s
TitleMinimal Hairpin Ribozyme in the Transition State with A38P Variation
Components
  • Loop A Substrate strand
  • Loop A and Loop B Ribozyme strand
  • Loop B of the Ribozyme Strand
KeywordsRNA / Structure-activity relationship / Nucleic Acid Conformation
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.84 Å
AuthorsLiberman, J.A. / Jenkins, J.L. / Krucinska, J. / Wedekind, J.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.
Authors: Liberman, J.A. / Guo, M. / Jenkins, J.L. / Krucinska, J. / Chen, Y. / Carey, P.R. / Wedekind, J.E.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Loop A Substrate strand
B: Loop A and Loop B Ribozyme strand
C: Loop B of the Ribozyme Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1946
Polymers19,7763
Non-polymers4183
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-26 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.966, 93.966, 134.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1-

U

-
Components

-
RNA chain , 3 types, 3 molecules ABC

#1: RNA chain Loop A Substrate strand


Mass: 4036.471 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain Loop A and Loop B Ribozyme strand


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain Loop B of the Ribozyme Strand


Mass: 5976.554 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% (w/v) PEG 2000 MME, 0.1M HEPES pH=7.0, 0.25 M Lithium Sulfate, 1mM Cobalt Hexamine, 2mM spermadine, vapor diffusion, Hanging Drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97885 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 5, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 8742 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.052 / Χ2: 1.36 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.84-2.946.60.7058201.167194.7
2.94-3.0670.4228391.259199.1
3.06-3.27.10.1788631.1131100
3.2-3.377.10.0948610.9831100
3.37-3.587.10.0858621.0711100
3.58-3.8570.0658651.2391100
3.85-4.2470.0498841.3341100
4.24-4.866.90.0438851.61199.9
4.86-6.126.80.0389131.838199.8
6.12-506.20.0349501.997194.6

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.84→30.097 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.33 / σ(F): 0 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 423 5.07 %
Rwork0.1863 --
obs0.1881 8345 94.69 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.875 Å2 / ksol: 0.244 e/Å3
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 89.0083 Å2 / Biso min: 61.87 Å2
Baniso -1Baniso -2Baniso -3
1--23.0949 Å20 Å20 Å2
2---23.0949 Å2-0 Å2
3---46.1898 Å2
Refinement stepCycle: LAST / Resolution: 2.84→30.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1308 19 3 1330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071500
X-RAY DIFFRACTIONf_angle_d0.9662330
X-RAY DIFFRACTIONf_chiral_restr0.058305
X-RAY DIFFRACTIONf_plane_restr0.00862
X-RAY DIFFRACTIONf_dihedral_angle_d18.036761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.84-3.24420.37111200.3392344246486
3.2442-4.08580.23141420.212713285599
4.0858-30.0970.19251610.1482865302699

+
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