[English] 日本語
Yorodumi
- PDB-4uu4: Crystal structure of LptH, the LptA homologous periplasmic compon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uu4
TitleCrystal structure of LptH, the LptA homologous periplasmic component of the conserved lipopolysaccharide transport device from Pseudomonas aeruginosa
ComponentsPERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTH
KeywordsTRANSPORT PROTEIN / LPTH / LPTA / LPS
Function / homology
Function and homology information


lipopolysaccharide transport => GO:0015920 / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function
Lipopolysaccharide (LPS) transport protein A like domain / Lipopolysaccharide export system protein LptA / lipopolysaccharide transport protein A fold / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lipopolysaccharide export system protein LptA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 Å
AuthorsBollati, M. / Villa, R. / Gourlay, L.J. / Barbiroli, A. / Deho, G. / Benedet, M. / Polissi, A. / Martorana, A. / Sperandeo, P. / Bolognesi, M. / Nardini, M.
CitationJournal: FEBS J. / Year: 2015
Title: Crystal Structure of Lpth, the Periplasmic Component of the Lipopolysaccharide Transport Machinery from Pseudomonas Aeruginosa.
Authors: Bollati, M. / Villa, R. / Gourlay, L.J. / Benedet, M. / Deho, G. / Polissi, A. / Barbiroli, A. / Martorana, A.M. / Sperandeo, P. / Bolognesi, M. / Marco, N.
History
DepositionJul 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTH


Theoretical massNumber of molelcules
Total (without water)19,1481
Polymers19,1481
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.000, 45.000, 146.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein PERIPLASMIC LIPOPOLYSACCHARIDE TRANSPORT PROTEIN LPTH


Mass: 19147.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q9HVV7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.94 Å3/Da / Density % sol: 40.6 % / Description: NONE
Crystal growpH: 7.5
Details: 20% 1,4-BUTANEDIOL, 0.1 M HEPES (PH 7.5), 0.2 M NACL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97241
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 2.75→45 Å / Num. obs: 4383 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R19

2r19


Resolution: 2.751→43.02 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2959 344 4.6 %
Rwork0.2351 --
obs0.2377 4331 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.751→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 0 32 1138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051120
X-RAY DIFFRACTIONf_angle_d0.9111518
X-RAY DIFFRACTIONf_dihedral_angle_d18.339429
X-RAY DIFFRACTIONf_chiral_restr0.07177
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7507-3.46540.27881740.24663581X-RAY DIFFRACTION100
3.4654-43.02570.30611700.22913526X-RAY DIFFRACTION99

+
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