[English] 日本語
Yorodumi
- PDB-6ije: Crystal structure of the type VI amidase immunity (Tai4) from Agr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ije
TitleCrystal structure of the type VI amidase immunity (Tai4) from Agrobacterium tumefaciens
ComponentsTai4
KeywordsANTITOXIN
Function / homologyRap1a immunity protein / Rap1a immunity proteins / Rap1a domain-containing protein
Function and homology information
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.
Authors: Fukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tai4
A: Tai4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8239
Polymers23,3882
Non-polymers4347
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-8 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.921, 57.756, 71.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 2 - 99 / Label seq-ID: 7 - 104

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

-
Components

#1: Protein Tai4


Mass: 11694.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_4314 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 48.3 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 33 % PEG 6000, 1.5 M lithium chloride, 100 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→53.92 Å / Num. obs: 32919 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 13 / Num. measured all: 203509 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.584.20.56815090.8070.3130.65494.7
8.49-53.925.90.0472550.9980.0210.05299.7

-
Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZFI

3zfi


Resolution: 1.55→44.96 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.375 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1556 4.7 %RANDOM
Rwork0.1742 ---
obs0.1753 31307 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.96 Å2 / Biso mean: 25.599 Å2 / Biso min: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--1.55 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 1.55→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 28 141 1667
Biso mean--48.4 35.2 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171526
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6482183
X-RAY DIFFRACTIONr_angle_other_deg1.6021.5773542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30122.22272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02321
Refine LS restraints NCS

Ens-ID: 1 / Number: 3044 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.01

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 107 -
Rwork0.239 2175 -
all-2282 -
obs--94.34 %

+
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://pdbjlvh1.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