[English] 日本語
Yorodumi
- PDB-4hz9: Crystal structure of the type VI native effector-immunity complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hz9
TitleCrystal structure of the type VI native effector-immunity complex Tae3-Tai3 from Ralstonia pickettii
Components
  • Putative cytoplasmic protein
  • Putative periplasmic protein
KeywordsHYDROLASE / protein-protein complex / endopeptidase / periplasmic space
Function / homology
Function and homology information


Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative cytoplasmic protein / Putative periplasmic protein
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDong, C. / Zhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3
Authors: Dong, C. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / She, Z. / Liu, G.F. / Shen, Y.Q. / Su, X.D. / Dong, Y.H.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)47,4433
Polymers47,4433
Non-polymers00
Water2,072115
1
A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein

A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)94,8866
Polymers94,8866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12950 Å2
ΔGint-28 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.166, 144.382, 129.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Putative cytoplasmic protein / toxin protein


Mass: 13100.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3260 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF2
#2: Protein Putative periplasmic protein / antitoxin protein


Mass: 17171.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3261 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01M ferric chloride hexahydrate, 0.1M tri-sodium citrate dihydrate pH5.6, 10% v/v jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 20876 / Num. obs: 20842 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 35.03 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2 / % possible all: 90.4

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZB

4hzb


Resolution: 2.4→48.286 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1069 5.13 %
Rwork0.1912 --
obs0.1933 20842 98.83 %
all-20876 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.889 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 117.98 Å2 / Biso mean: 36.3322 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-5.8127 Å2-0 Å2-0 Å2
2---4.3926 Å2-0 Å2
3----1.4201 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 0 115 3033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073010
X-RAY DIFFRACTIONf_angle_d1.0224107
X-RAY DIFFRACTIONf_dihedral_angle_d13.1821070
X-RAY DIFFRACTIONf_chiral_restr0.073427
X-RAY DIFFRACTIONf_plane_restr0.005534
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4004-2.50960.41651260.3392266239293
2.5096-2.64190.33631370.24642408254598
2.6419-2.80740.26421290.200624822611100
2.8074-3.02420.24151230.190224812604100
3.0242-3.32840.27611270.200425002627100
3.3284-3.80990.23871390.19625002639100
3.8099-4.79940.16871580.14624982656100
4.7994-48.29560.19791300.177526382768100
Refinement TLS params.Method: refined / Origin x: 5.2936 Å / Origin y: 15.5327 Å / Origin z: -0.0079 Å
111213212223313233
T0.0998 Å20.0222 Å2-0.0064 Å2-0.0842 Å20.0174 Å2--0.1192 Å2
L0.7266 °2-0.0042 °2-0.0095 °2-1.2267 °2-0.0519 °2--1.3558 °2
S-0.0179 Å °0.0246 Å °0.1796 Å °-0.042 Å °-0.0717 Å °-0.0304 Å °-0.3034 Å °-0.0497 Å °0.0587 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 119
2X-RAY DIFFRACTION1allB29 - 151
3X-RAY DIFFRACTION1allC30 - 151
4X-RAY DIFFRACTION1allA201 - 241
5X-RAY DIFFRACTION1allB201 - 247
6X-RAY DIFFRACTION1allC201 - 227

+
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