[English] 日本語
Yorodumi
- PDB-7p6m: Hydrogenated refolded hen egg-white lysozyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p6m
TitleHydrogenated refolded hen egg-white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / HEWL / refolded / hydrogenated / recombinant
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å
AuthorsRamos, J. / Laux, V. / Haertlein, M. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme.
Authors: Ramos, J. / Laux, V. / Haertlein, M. / Forsyth, V.T. / Mossou, E. / Larsen, S. / Langkilde, A.E.
History
DepositionJul 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,00211
Polymers14,3881
Non-polymers61410
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, 14365 Da
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint7 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.120, 30.700, 33.540
Angle α, β, γ (deg.)88.970, 72.770, 69.500
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14388.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.9 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.5
Details: 0.05 M sodium acetate pH 4.5, 0.3 M sodium nitrate, micro seeds of G. gallus HEWL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.700001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700001 Å / Relative weight: 1
ReflectionResolution: 0.89→22.46 Å / Num. obs: 68446 / % possible obs: 96.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 7.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Rrim(I) all: 0.098 / Net I/σ(I): 7.4
Reflection shellResolution: 0.89→0.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.647 / Num. unique obs: 6717 / CC1/2: 0.799 / Rpim(I) all: 0.398 / Rrim(I) all: 0.762 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
SHELXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 7ave

7ave


Resolution: 0.89→22.46 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1531 3423 5 %
Rwork0.1251 --
obs-65023 96.2 %
Displacement parametersBiso max: 147.69 Å2 / Biso mean: 13.9443 Å2 / Biso min: 3.95 Å2
Refinement stepCycle: LAST / Resolution: 0.89→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 40 145 1190

+
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