[English] 日本語
Yorodumi
- PDB-4gqd: DNA Holliday junction stabilized by chlorine halogen bond. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gqd
TitleDNA Holliday junction stabilized by chlorine halogen bond.
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
KeywordsDNA / DNA Holliday junction / halogen bond
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsCarter, M. / Ho, P.S.
CitationJournal: Biochemistry / Year: 2013
Title: Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.
Authors: Carter, M. / Voth, A.R. / Scholfield, M.R. / Rummel, B. / Sowers, L.C. / Ho, P.S.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 13, 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_alt_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_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2927
Polymers12,2234
Non-polymers693
Water1,67593
1
A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
D: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,58414
Polymers24,4468
Non-polymers1386
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)65.692, 23.565, 37.286
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

21D-113-

HOH

DetailsThe biological assembly of this structure is the four stranded DNA Holliday junction. DNA Holliday junctions are generated from the two stranded asymmetric subunit through the two-fold symmetry operator at the center of the four-stranded junction.

-
Components

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


Mass: 3081.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#2: DNA chain DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')


Mass: 3029.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD., VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 21, 2009
RadiationMonochromator: ROSENBAUM-ROCK SI(111) SAGITALLY FOCUSED MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.94→30.68 Å / Num. all: 4793 / Num. obs: 3538 / % possible obs: 73.8 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 4.6 Å2
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 1.02 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.25 / Num. unique all: 638 / Rsym value: 0.268 / % possible all: 54.2

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ORG

2org


Resolution: 1.94→30.68 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 28646.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.4 / σ(I): 2 / Stereochemistry target values: CNS / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3 174 5.2 %RANDOM
Rwork0.264 ---
obs0.264 3323 81 %-
all-4793 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.8587 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.07 Å2
2--5.95 Å20 Å2
3----7.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 1.94→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 3 93 904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.162.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.127 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.492 15 4.1 %
Rwork0.379 351 -
obs--54.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1voth_topolovoth_topolo
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

+
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