[English] 日本語
Yorodumi
- PDB-3nyp: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nyp
TitleA bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / QUADRUPLEX / OXTYRICHA NOVA / BSU-6039 / BSU6039 / ANTI-PARALLEL / BIMOLECULAR / MACROMOLECULE / G-QUADRUPLEX / TELOMERE / ACRIDINE
Function / homology: / Chem-RNR / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsCampbell, N.H. / Neidle, S.
CitationJournal: Org.Biomol.Chem. / Year: 2011
Title: Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA.
Authors: Campbell, N.H. / Smith, D.L. / Reszka, A.P. / Neidle, S. / O'Hagan, D.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_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: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2637
Polymers7,6112
Non-polymers6525
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 44.460, 28.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-147-

HOH

-
Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This telomeric sequence occurs naturally in the organism Oxytricha nova
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-RNR / 3,6-bis(3-(3'-(R)-fluoropyrrolindino)propionamido)acridine / N,N'-acridine-3,6-diylbis{3-[(3R)-3-fluoropyrrolidin-1-yl]propanamide}


Mass: 495.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31F2N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The 5 Ul drop contained 1.2 mM quadruplex DNA, 1.2 mM ligand, 4% MPD, 4 mM potassium chloride, 4 mM magnesium chloride, 4 mM sodium chloride, 4 mM lithium sulphate, 3.2 mM spermine.4HCl and ...Details: The 5 Ul drop contained 1.2 mM quadruplex DNA, 1.2 mM ligand, 4% MPD, 4 mM potassium chloride, 4 mM magnesium chloride, 4 mM sodium chloride, 4 mM lithium sulphate, 3.2 mM spermine.4HCl and 16 mM potassium cacodylate buffer at pH 6.5. This was equilibrated against a reservoir well solution of 500 Ul of 45% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 1.18→21.99 Å / Num. all: 23982 / Num. obs: 23982 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.18-1.243.50.125.71199134230.1297.8
1.24-1.323.60.0897.41191932890.08998.5
1.32-1.413.60.0748.81139131360.07499.2
1.41-1.523.70.0797.71068029140.07999.3
1.52-1.673.70.0629.1993027200.06299.6
1.67-1.863.70.04910.6901924630.04999.3
1.86-2.153.60.04712.2788121860.04799.7
2.15-2.643.30.05410.5611418420.05498.3
2.64-3.733.40.03715.1480814010.03794.5
3.73-20.7482.80.03217.817146080.03268.3

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L1H

1l1h


Resolution: 1.179→21.99 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.13 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 1183 5.08 %Random
Rwork0.1647 ---
obs0.1658 23275 94.59 %-
all-23275 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.946 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 56.09 Å2 / Biso mean: 14.8626 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.5525 Å20 Å2-0 Å2
2--1.2304 Å20 Å2
3----2.7829 Å2
Refinement stepCycle: LAST / Resolution: 1.179→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 40 177 723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024609
X-RAY DIFFRACTIONf_angle_d2.125937
X-RAY DIFFRACTIONf_chiral_restr0.14194
X-RAY DIFFRACTIONf_plane_restr0.02227
X-RAY DIFFRACTIONf_dihedral_angle_d31.085265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.179-1.23270.28081400.198324402580244086
1.2327-1.29760.22581280.166325972725259790
1.2976-1.37890.19531420.153926732815267393
1.3789-1.48540.21131610.160227432904274395
1.4854-1.63480.1781510.157428112962281197
1.6348-1.87130.16671490.132928703019287098
1.8713-2.35720.17171610.151329053066290599
2.3572-21.99340.17161510.173130533204305398

+
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