[English] 日本語
Yorodumi
- PDB-4f4m: Structure of the type VI peptidoglycan amidase effector Tse1 (C30... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f4m
TitleStructure of the type VI peptidoglycan amidase effector Tse1 (C30A) from Pseudomonas aeruginosa
Componentspapain peptidoglycan amidase effector Tse1
KeywordsHydrolase regulator / papain peptidoglycan amidase effector / amidase / Tsi1
Function / homology
Function and homology information


gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane
Similarity search - Function
endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan amidase Tse1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.677 Å
AuthorsChou, S. / Mougous, J.D.
CitationJournal: Cell Rep / Year: 2012
Title: Structure of a peptidoglycan amidase effector targeted to Gram-negative bacteria by the type VI secretion system.
Authors: Chou, S. / Bui, N.K. / Russell, A.B. / Lexa, K.W. / Gardiner, T.E. / LeRoux, M. / Vollmer, W. / Mougous, J.D.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Structure summary
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: papain peptidoglycan amidase effector Tse1
B: papain peptidoglycan amidase effector Tse1
C: papain peptidoglycan amidase effector Tse1
D: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)69,0224
Polymers69,0224
Non-polymers00
Water00
1
A: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: papain peptidoglycan amidase effector Tse1


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.018, 108.857, 82.531
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
papain peptidoglycan amidase effector Tse1


Mass: 17255.490 Da / Num. of mol.: 4 / Fragment: Tse1 C30A / Mutation: C30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1844 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained by sitting drop vapor diffusion at 25 oC from a 1:1 mixture of 10 mg/mL protein with 0.2 M sodium thiocyanate, 0.1 M HEPES (pH 7.5), 20% PEG3350 for 3 days. Crystals ...Details: Crystals were obtained by sitting drop vapor diffusion at 25 oC from a 1:1 mixture of 10 mg/mL protein with 0.2 M sodium thiocyanate, 0.1 M HEPES (pH 7.5), 20% PEG3350 for 3 days. Crystals were immersed in mother liquor containing 20% glycerol, mounted, and flash frozen in liquid N2. , VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.677→65.69 Å / Num. all: 19092 / Num. obs: 19072 / % possible obs: 100 % / Biso Wilson estimate: 18.61 Å2 / Rmerge(I) obs: 0.136

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXPhasermodel building
PHENIX(phenix.refine: dev_1047)refinement
XDSdata reduction
PHENIXPhaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.677→65.69 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.243 981 5.15 %Random
Rwork0.2035 ---
all0.234 19092 --
obs0.2056 19064 95.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.677→65.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 0 0 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084452
X-RAY DIFFRACTIONf_angle_d1.1126032
X-RAY DIFFRACTIONf_dihedral_angle_d14.1211568
X-RAY DIFFRACTIONf_chiral_restr0.078652
X-RAY DIFFRACTIONf_plane_restr0.003784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6767-2.81790.28021210.23992387X-RAY DIFFRACTION89
2.8179-2.99440.30521400.23662626X-RAY DIFFRACTION97
2.9944-3.22560.30621530.242618X-RAY DIFFRACTION97
3.2256-3.55020.27431530.21492608X-RAY DIFFRACTION98
3.5502-4.06380.19991330.19352646X-RAY DIFFRACTION97
4.0638-5.11970.19951420.16672627X-RAY DIFFRACTION97
5.1197-65.71020.20661390.18042571X-RAY DIFFRACTION94

+
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