[English] 日本語
Yorodumi
- PDB-3hr3: Interplay of Structure, Hydration and Thermal Stability in Formac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hr3
TitleInterplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA
Components5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'
KeywordsDNA / RNA / formacetal-DNA / RNA hydration
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA.
Authors: Kolarovic, A. / Schweizer, E. / Greene, E. / Gironda, M. / Pallan, P.S. / Egli, M. / Rozners, E.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,0111
Polymers3,0111
Non-polymers00
Water41423
1
A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'

A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0222
Polymers6,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2100 Å2
ΔGint4 kcal/mol
Surface area3470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.199, 33.199, 68.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: DNA chain 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Mass: 3011.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesize deoxyribonucleotide, US4 = Formacetal linked thymidine and 2'-deoxyadenosine (TfA)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v) , VAPOR DIFFUSION, ...Details: Sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2009 / Details: Monochromator Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 4208 / Num. obs: 4006 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.187 / Num. unique all: 139 / % possible all: 72.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single strand from the duplex of PDB ID 411D.

411d


Resolution: 1.75→29.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.139 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28185 291 7.3 %RANDOM
Rwork0.22786 ---
obs0.23147 3714 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.242 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 0 23 224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021225
X-RAY DIFFRACTIONr_angle_refined_deg3.0372.974344
X-RAY DIFFRACTIONr_chiral_restr0.120.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02104
X-RAY DIFFRACTIONr_scbond_it3.5153225
X-RAY DIFFRACTIONr_scangle_it4.5194.5343
X-RAY DIFFRACTIONr_rigid_bond_restr3.283225
X-RAY DIFFRACTIONr_sphericity_free7.99329
X-RAY DIFFRACTIONr_sphericity_bonded6.0833201
LS refinement shellResolution: 1.753→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 19 -
Rwork0.376 199 -
obs--73.65 %

+
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