[English] 日本語
Yorodumi
- PDB-6bmd: RNA hairpin containing GpppG-oligo to mimic intermediate formed b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bmd
TitleRNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper
Components
  • RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
KeywordsRNA / GpppG / helper / intermediate
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, W. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howar United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / Szostak, J.W.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
B: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
C: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
D: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
E: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
F: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,2946
Polymers32,2946
Non-polymers00
Water66737
1
A: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
B: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-0 kcal/mol
Surface area6150 Å2
MethodPISA
2
C: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
D: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint1 kcal/mol
Surface area6140 Å2
MethodPISA
3
E: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
F: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint1 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.392, 63.759, 65.840
Angle α, β, γ (deg.)90.00, 122.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: RNA chain RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')


Mass: 7853.808 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Mass: 2910.738 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5

-
Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7315 / % possible obs: 95.9 % / Redundancy: 4.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.094 / Rrim(I) all: 0.213 / Rsym value: 0.144 / Χ2: 0.654 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 557 / CC1/2: 0.904 / Rpim(I) all: 0.198 / Rrim(I) all: 0.429 / Rsym value: 0.334 / Χ2: 0.571 / % possible all: 74.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZ6

5uz6


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.539 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 392 5.4 %RANDOM
Rwork0.18352 ---
obs0.1861 6922 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.407 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.05 Å2
2--0.12 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2157 0 37 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132400
X-RAY DIFFRACTIONr_bond_other_d0.0190.021981
X-RAY DIFFRACTIONr_angle_refined_deg2.061.5043723
X-RAY DIFFRACTIONr_angle_other_deg2.3973.0732385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1750.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7852.8532399
X-RAY DIFFRACTIONr_scbond_other1.7852.8532400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7074.2783723
X-RAY DIFFRACTIONr_long_range_B_refined3.86227.6123458
X-RAY DIFFRACTIONr_long_range_B_other3.86127.6093459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 22 -
Rwork0.264 371 -
obs--71.2 %

+
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