[English] 日本語
Yorodumi
- PDB-7lnf: 3'-deoxy modification at 3' end of RNA primer complex with guanos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lnf
Title3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GDO))-3')
KeywordsRNA / nonenzymatic RNA extension
Function / homology: / 3'-deoxy-guanosine 5'-monophosphate / DIGUANOSINE-5'-TRIPHOSPHATE / Chem-LCC / Chem-LCG / Chem-LKC / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsFang, Z. / Giurgiu, C. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1607034 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Authors: Giurgiu, C. / Fang, Z. / Aitken, H.R.M. / Kim, S.C. / Pazienza, L. / Mittal, S. / Szostak, J.W.
History
DepositionFeb 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GDO))-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GDO))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,11524
Polymers8,8452
Non-polymers5,26922
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-49 kcal/mol
Surface area5610 Å2
Unit cell
Length a, b, c (Å)46.822, 46.822, 83.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-107-

MG

21A-259-

HOH

31B-258-

HOH

41B-262-

HOH

-
Components

-
RNA chain , 1 types, 2 molecules AB

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


Mass: 4422.683 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 8 types, 145 molecules

#2: Chemical
ChemComp-LCC / [(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE


Type: RNA linking / Mass: 349.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N3O8P
#3: Chemical ChemComp-LCG / [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE


Type: RNA linking / Mass: 375.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N5O8P
#4: Chemical ChemComp-GDO / 3'-deoxy-guanosine 5'-monophosphate


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LKC / 4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE


Type: RNA linking / Mass: 269.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N3O5
#6: Chemical ChemComp-GP3 / DIGUANOSINE-5'-TRIPHOSPHATE


Mass: 788.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27N10O18P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.02 M Magnesium sulfate hydrate, 0.002 M Cobalt (II) chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine

-
Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 13195 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Χ2: 0.935 / Net I/σ(I): 23.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 658 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.142 / Rrim(I) all: 0.418 / Χ2: 0.732 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UEE

5uee


Resolution: 1.652→27.748 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.925 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2394 553 4.69 %
Rwork0.2081 11237 -
all0.21 --
obs-11790 89.008 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0.001 Å2-0 Å2
2---0.002 Å20 Å2
3---0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.652→27.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 378 330 123 831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.018794
X-RAY DIFFRACTIONr_bond_other_d0.0310.025352
X-RAY DIFFRACTIONr_angle_refined_deg2.8762.1351192
X-RAY DIFFRACTIONr_angle_other_deg4.0993.208826
X-RAY DIFFRACTIONr_chiral_restr0.4610.2140
X-RAY DIFFRACTIONr_chiral_restr_other1.8830.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023148
X-RAY DIFFRACTIONr_nbd_refined0.0860.267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.2500
X-RAY DIFFRACTIONr_nbtor_refined0.2510.2303
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2750.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0820.211
X-RAY DIFFRACTIONr_nbd_other0.1920.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.215
X-RAY DIFFRACTIONr_scbond_it1.8911.56794
X-RAY DIFFRACTIONr_scbond_other1.891.56795
X-RAY DIFFRACTIONr_scangle_it2.2752.3521192
X-RAY DIFFRACTIONr_scangle_other2.2742.3511193
X-RAY DIFFRACTIONr_lrange_it3.84514.5061101
X-RAY DIFFRACTIONr_lrange_other3.69413.8271066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.652-1.6940.296190.213407X-RAY DIFFRACTION44.2368
1.694-1.7410.13518493X-RAY DIFFRACTION54.2463
1.741-1.7910.227310.195547X-RAY DIFFRACTION63.8674
1.791-1.8460.261500.205718X-RAY DIFFRACTION88.0734
1.846-1.9070.13125828X-RAY DIFFRACTION99.4173
1.907-1.9740.255430.222783X-RAY DIFFRACTION100
1.974-2.0480.302210.237792X-RAY DIFFRACTION100
2.048-2.1320.315420.234746X-RAY DIFFRACTION100
2.132-2.2270.264440.236699X-RAY DIFFRACTION100
2.227-2.3350.299290.224684X-RAY DIFFRACTION100
2.335-2.4610.1829645X-RAY DIFFRACTION100
2.461-2.610.296400.23610X-RAY DIFFRACTION100
2.61-2.7910.336410.229571X-RAY DIFFRACTION100
2.791-3.0140.289220.212533X-RAY DIFFRACTION99.2844
3.014-3.3010.17223508X-RAY DIFFRACTION97.9705
3.301-3.690.258200.189455X-RAY DIFFRACTION98.7526
3.69-4.2590.16317417X-RAY DIFFRACTION98.4127
4.259-5.2130.189250.176350X-RAY DIFFRACTION99.4695
5.213-7.3580.20180.182286X-RAY DIFFRACTION99.3243
7.358-27.7480.1586165X-RAY DIFFRACTION89.5288

+
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