[English] 日本語
Yorodumi
- PDB-3bbm: Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bbm
TitleMinimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site
Components
  • Loop A Substrate strand
  • Loop A and Loop B Ribozyme strand
  • Loop B S-turn strand
KeywordsRNA / hairpin ribozyme / phosphoryl transfer / 2'O-methyl / small ribozyme
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsMacElrevey, C. / Krucinska, J. / Wedekind, J.E.
CitationJournal: Rna / Year: 2008
Title: Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Authors: MacElrevey, C. / Salter, J.D. / Krucinska, J. / Wedekind, J.E.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

-
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 S-turn strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3767
Polymers19,7973
Non-polymers5794
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-28 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.650, 93.650, 133.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
RNA chain , 3 types, 3 molecules ABC

#1: RNA chain Loop A Substrate strand


Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado
#2: RNA chain Loop A and Loop B Ribozyme strand


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado
#3: RNA chain Loop B S-turn strand


Mass: 5967.544 Da / Num. of mol.: 1 / Mutation: A38G, U39C / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado

-
Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


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.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.27 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2K MME11
2Li2SO411
3sodium cacodylate11
4spermidine11
5cobalt hexaammine11
6PEG 2K MME12
7Li2SO412
8sodium cacodylate12
9spermidine12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2006 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→30.86 Å / Num. all: 10593 / Num. obs: 10427 / % possible obs: 98.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 89.5 Å2 / Rsym value: 0.049 / Net I/σ(I): 20.5
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1023 / Rsym value: 0.399 / % possible all: 98.9

-
Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2OUE

2oue


Resolution: 2.65→29.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 678076.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber / Details: alternate conformation at resi 1 chain A
RfactorNum. reflection% reflectionSelection details
Rfree0.217 644 6.2 %RANDOM
Rwork0.204 ---
obs0.206 10416 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 85.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.99 Å2-0.34 Å20 Å2
2---11.99 Å20 Å2
3---23.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-30.85 Å
Luzzati sigma a0.6 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1309 26 7 1342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d16.4
X-RAY DIFFRACTIONc_improper_angle_d3.19
LS refinement shellResolution: 2.65→2.92 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.46 154 6 %
Rwork0.457 2416 -
obs-2570 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rna0107.top
X-RAY DIFFRACTION2dna-rna0107.parwater.top
X-RAY DIFFRACTION3cobalt.parcobalt.top
X-RAY DIFFRACTION4ion.paramion.top

+
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