[English] 日本語
Yorodumi
- PDB-5yqr: Crystal structure of the PH-like domain of Lam6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yqr
TitleCrystal structure of the PH-like domain of Lam6
ComponentsEndolysin/Membrane-anchored lipid-binding protein LAM6 fusion protein
KeywordsTRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / LTC1
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / nucleus-vacuole junction / vacuole-mitochondrion membrane contact site / sterol transfer activity / sterol binding / mitochondria-associated endoplasmic reticulum membrane contact site / cortical endoplasmic reticulum / viral release from host cell by cytolysis / peptidoglycan catabolic process ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / nucleus-vacuole junction / vacuole-mitochondrion membrane contact site / sterol transfer activity / sterol binding / mitochondria-associated endoplasmic reticulum membrane contact site / cortical endoplasmic reticulum / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / : / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme ...VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / : / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endolysin / Membrane-anchored lipid-binding protein LAM6
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsTong, J. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4004914 Korea, Republic Of
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites
Authors: Tong, J. / Manik, M.K. / Im, Y.J.
History
DepositionNov 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin/Membrane-anchored lipid-binding protein LAM6 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1402
Polymers31,7251
Non-polymers4141
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.543, 60.103, 105.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endolysin/Membrane-anchored lipid-binding protein LAM6 fusion protein / Lysis protein / Lysozyme / Muramidase / Lipid transfer at contact site protein 1 / Lipid transfer ...Lysis protein / Lysozyme / Muramidase / Lipid transfer at contact site protein 1 / Lipid transfer protein anchored at membrane contact sites 1


Mass: 31725.223 Da / Num. of mol.: 1 / Mutation: R12G,D20N, C54T, C97A, I137R
Source method: isolated from a genetically manipulated source
Details: The N-termial T4 lysozyme (residue 2-160) tag fusion.The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272),The N-termial T4 lysozyme (residue ...Details: The N-termial T4 lysozyme (residue 2-160) tag fusion.The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272),The N-termial T4 lysozyme (residue 2-160) tag fusion. The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272)
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Plasmid: pHis-T4L / Strain: ATCC 204508 / S288c / Gene: LAM6, LTC1, YLR072W
Details (production host): N-terminal T4 Lysozyme tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, UniProt: Q08001, lysozyme
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Water ChemComp-HOH / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-HCl pH 7.0, 10% PEG8000, 0.1M Na3Citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15204 / % possible obs: 99 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 48.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 9.7 / Num. unique obs: 727 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9N

4n9n


Resolution: 2.402→30.374 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 750 4.95 %random selection
Rwork0.2181 ---
obs0.2207 15156 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→30.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 28 32 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082247
X-RAY DIFFRACTIONf_angle_d1.083025
X-RAY DIFFRACTIONf_dihedral_angle_d15.8211358
X-RAY DIFFRACTIONf_chiral_restr0.056333
X-RAY DIFFRACTIONf_plane_restr0.006380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.402-2.58740.40671240.2872855X-RAY DIFFRACTION99
2.5874-2.84760.31851650.26242845X-RAY DIFFRACTION100
2.8476-3.25930.29091370.24712888X-RAY DIFFRACTION100
3.2593-4.10470.23831750.19922891X-RAY DIFFRACTION100
4.1047-30.37660.2491490.19752927X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 25.0507 Å / Origin y: 56.3488 Å / Origin z: 44.0798 Å
111213212223313233
T0.3484 Å20.0986 Å20.0745 Å2-0.3996 Å20.0603 Å2--0.3431 Å2
L0.6361 °20.0588 °20.2117 °2-2.0712 °21.1176 °2--1.4049 °2
S-0.1056 Å °-0.1783 Å °-0.0412 Å °0.302 Å °0.1529 Å °0.0432 Å °0.0872 Å °-0.0358 Å °-0.028 Å °
Refinement TLS groupSelection details: all

+
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