[English] 日本語
Yorodumi
- PDB-4osh: Crystal structure of the TAL effector dHax3 with NI RVD at 2.2 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4osh
TitleCrystal structure of the TAL effector dHax3 with NI RVD at 2.2 angstrom resolution
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
  • Hax3
KeywordsDNA binding protein/DNA / DNA binding protein / DNA / DNA binding protein-DNA complex
Function / homology: / TAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsDeng, D. / Wu, J.P. / Yan, C.Y. / Pan, X.J. / Yan, N.
CitationJournal: Protein Cell / Year: 2014
Title: Revisiting the TALE repeat
Authors: Deng, D. / Yan, C.Y. / Wu, J.P. / Pan, X.J. / Yan, N.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,3876
Polymers124,3876
Non-polymers00
Water5,080282
1
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1933
Polymers62,1933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-67 kcal/mol
Surface area22630 Å2
MethodPISA
2
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1933
Polymers62,1933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-65 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.529, 80.987, 89.083
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hax3


Mass: 51780.586 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505I,S539G,N572H,S573D,H606N,D607G,N640H,I641D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria)
Gene: hax3 / Plasmid: PET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 48.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%-15% PEG 3350, 12% ethanol, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 58949 / Num. obs: 58921 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 30.92 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.283.30.5882.45364190.5
2.28-2.373.60.473.45869198.8
2.37-2.483.60.3864.35902199.1
2.48-2.613.60.3155.55918199.3
2.61-2.773.60.2427.45907199.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 2.201→36.633 Å / FOM work R set: 0.8092 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2984 5.06 %
Rwork0.2049 55937 -
obs0.207 58921 99.26 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.727 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 141.06 Å2 / Biso mean: 43.56 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.5825 Å20 Å2-9.468 Å2
2--0.1765 Å2-0 Å2
3---5.1383 Å2
Refinement stepCycle: LAST / Resolution: 2.201→36.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 1246 0 282 8559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088531
X-RAY DIFFRACTIONf_angle_d1.28911896
X-RAY DIFFRACTIONf_chiral_restr0.0761460
X-RAY DIFFRACTIONf_plane_restr0.0081355
X-RAY DIFFRACTIONf_dihedral_angle_d20.3483201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2008-2.23690.32931380.27032483262194
2.2369-2.27540.30531490.24792621277099
2.2754-2.31680.25811230.23522692281599
2.3168-2.36140.27031260.22222622274899
2.3614-2.40960.2951520.2222655280799
2.4096-2.46190.26271490.2192618276799
2.4619-2.51920.2861290.21632637276699
2.5192-2.58220.28051390.22912657279699
2.5822-2.6520.30921380.222326642802100
2.652-2.730.29811500.226626892839100
2.73-2.81810.25691720.21226362808100
2.8181-2.91880.27751210.225627072828100
2.9188-3.03560.29241420.232626532795100
3.0356-3.17370.2561360.21827042840100
3.1737-3.34090.23481480.214626712819100
3.3409-3.550.22721480.196926882836100
3.55-3.82390.1991340.185926832817100
3.8239-4.20820.23971440.176826952839100
4.2082-4.81590.21390.170627022841100
4.8159-6.06310.23761690.215126942863100
6.0631-36.63840.21731380.18627662904100
Refinement TLS params.Method: refined / Origin x: 5.2594 Å / Origin y: -14.388 Å / Origin z: -23.3427 Å
111213212223313233
T0.1237 Å20.0031 Å20.002 Å2-0.1353 Å20.0118 Å2--0.1261 Å2
L0.3857 °20.0864 °20.1114 °2-0.15 °2-0.0432 °2--0.0934 °2
S0.0271 Å °-0.0924 Å °-0.0352 Å °0.0188 Å °-0.0109 Å °-0.0066 Å °-0.0038 Å °-0.0316 Å °0.0008 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