[English] 日本語
Yorodumi
- PDB-4gg4: Crystal structure of the TAL effector dHax3 bound to specific DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gg4
TitleCrystal structure of the TAL effector dHax3 bound to specific DNA-RNA hybrid
Components
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
  • Hax3
  • RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*UP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA/RNA / tandem repeat / TAL effector / sequence specific DNA binding protein / DNA duplex / DNA-RNA hybrid / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


host cell nucleus / extracellular region
Similarity search - Function
: / TAL effector repeat / TAL effector repeat
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Hax3
Similarity search - Component
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsYin, P. / Deng, D. / Yan, C.Y. / Pan, X.J. / Yan, N. / Shi, Y.G.
CitationJournal: Cell Rep / Year: 2012
Title: Specific DNA-RNA hybrid recognition by TAL effectors
Authors: Yin, P. / Deng, D. / Yan, C. / Pan, X.J. / Xi, J.J. / Yan, N. / Shi, Y.
History
DepositionAug 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*UP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,4513
Polymers62,4513
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-59 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.735, 99.735, 134.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Hax3


Mass: 51780.586 Da / Num. of mol.: 1 / Fragment: TAL effector, UNP residues 231-720 / Mutation: multiple mutations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria)
Gene: hax3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72
#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 5070.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA oligo was ordered from Takara
#3: RNA chain RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*UP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5600.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA oligo was ordered from Takara
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 11% PEG 3350 (w/v), 12% ethanol, 0.1M MES pH6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2011
RadiationMonochromator: Si 111 CHANNE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00915 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 26222 / Num. obs: 25803 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 47.42 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 2.501→31.725 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8139 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1327 5.15 %RANDOM
Rwork0.1929 ---
all0.1954 26222 --
obs0.1954 25773 98.37 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.337 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 124.82 Å2 / Biso mean: 50.2915 Å2 / Biso min: 22.31 Å2
Baniso -1Baniso -2Baniso -3
1-7.5378 Å20 Å2-0 Å2
2--7.5378 Å20 Å2
3----9.6634 Å2
Refinement stepCycle: LAST / Resolution: 2.501→31.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 687 0 56 4265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074338
X-RAY DIFFRACTIONf_angle_d1.1826063
X-RAY DIFFRACTIONf_dihedral_angle_d17.2751662
X-RAY DIFFRACTIONf_chiral_restr0.068756
X-RAY DIFFRACTIONf_plane_restr0.007679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.501-2.60110.33141470.29052690283798
2.6011-2.71950.36711430.28432735287899
2.7195-2.86270.32731550.24852719287499
2.8627-3.0420.25721570.24862738289599
3.042-3.27660.23041550.21332708286399
3.2766-3.6060.26221580.19842714287299
3.606-4.12680.22911340.17412740287499
4.1268-5.19560.21281310.15712733286498
5.1956-31.72730.19621470.16042669281696
Refinement TLS params.Method: refined / Origin x: 49.8698 Å / Origin y: -16.5325 Å / Origin z: -10.3553 Å
111213212223313233
T0.2761 Å20.011 Å20.0303 Å2-0.252 Å20.0035 Å2--0.2925 Å2
L0.6327 °20.1214 °2-0.0293 °2-0.4829 °2-0.1795 °2--0.7052 °2
S-0.0043 Å °0.0056 Å °-0.0027 Å °0.0638 Å °0.0445 Å °0.0422 Å °0.0044 Å °0.0695 Å °0 Å °
Refinement TLS groupSelection details: all

+
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