[English] 日本語
Yorodumi
- PDB-4m5f: complex structure of Tse3-Tsi3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m5f
Titlecomplex structure of Tse3-Tsi3
Components(Uncharacterized protein) x 2
KeywordsHYDROLASE INHIBITOR / Beta-sheets
Function / homology
Function and homology information


host cell membrane / lysozyme / lysozyme activity / extracellular region / metal ion binding / membrane
Similarity search - Function
Jelly Rolls - #1690 / : / : / T6SS, Peptidoglycan muramidase Tse3, catalytic domain / T6SS, Peptidoglycan muramidase Tse3, N-terminal domain / : / : / Type six secretion immunity 3 domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls ...Jelly Rolls - #1690 / : / : / T6SS, Peptidoglycan muramidase Tse3, catalytic domain / T6SS, Peptidoglycan muramidase Tse3, N-terminal domain / : / : / Type six secretion immunity 3 domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Immune protein Tsi3 / Peptidoglycan muramidase Tse3
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGu, L.C.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex from Pseudomonas aeruginosa reveal a calcium-dependent membrane-binding mechanism
Authors: Lu, D. / Shang, G. / Zhang, H. / Yu, Q. / Cong, X. / Yuan, J. / He, F. / Zhu, C. / Zhao, Y. / Yin, K. / Chen, Y. / Hu, J. / Zhang, X. / Yuan, Z. / Xu, S. / Hu, W. / Cang, H. / Gu, L.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Derived calculations
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9618
Polymers57,5552
Non-polymers4056
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-53 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.242, 92.242, 169.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Uncharacterized protein


Mass: 43520.977 Da / Num. of mol.: 1 / Fragment: fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3484 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC5
#2: Protein Uncharacterized protein


Mass: 14034.423 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3485 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / pH: 7.8
Details: 0.8M Na2HPO4/KH2PO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26198 / % possible obs: 85 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 95

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m5e

4m5e


Resolution: 2.5→33.34 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1956 7.7 %
Rwork0.193 --
obs0.197 25394 97.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.01 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3187 Å20 Å2-0 Å2
2--5.3187 Å2-0 Å2
3----10.6374 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 18 160 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084129
X-RAY DIFFRACTIONf_angle_d1.1545622
X-RAY DIFFRACTIONf_dihedral_angle_d16.4511521
X-RAY DIFFRACTIONf_chiral_restr0.073619
X-RAY DIFFRACTIONf_plane_restr0.005748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56060.31131320.22311550X-RAY DIFFRACTION92
2.5606-2.62980.24741330.20141590X-RAY DIFFRACTION95
2.6298-2.70720.28741330.19941605X-RAY DIFFRACTION95
2.7072-2.79450.26581370.1921608X-RAY DIFFRACTION95
2.7945-2.89440.27611350.20511646X-RAY DIFFRACTION97
2.8944-3.01020.25921380.19661652X-RAY DIFFRACTION97
3.0102-3.14710.27521370.20951676X-RAY DIFFRACTION98
3.1471-3.31290.27911400.20211671X-RAY DIFFRACTION98
3.3129-3.52020.291380.19921657X-RAY DIFFRACTION97
3.5202-3.79170.24571420.19941673X-RAY DIFFRACTION98
3.7917-4.17260.21131430.17711710X-RAY DIFFRACTION98
4.1726-4.77480.20551450.15631742X-RAY DIFFRACTION100
4.7748-6.010.23921460.21251772X-RAY DIFFRACTION100
6.01-33.33770.20381570.18781886X-RAY DIFFRACTION100

+
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