[English] 日本語
Yorodumi
- PDB-7ap7: Structure of the W64R amyloidogenic variant of human lysozyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ap7
TitleStructure of the W64R amyloidogenic variant of human lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / amyloidoses
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsVettore, N. / Herman, R. / Kerff, F. / Charlier, P. / Sauvage, E. / Brans, A. / Morray, J. / Dobson, C. / Kumita, J. / Dumoulin, M.
CitationJournal: Biophys.Chem. / Year: 2021
Title: Characterisation of the structural, dynamic and aggregation properties of the W64R amyloidogenic variant of human lysozyme.
Authors: Vettore, N. / Moray, J. / Brans, A. / Herman, R. / Charlier, P. / Kumita, J.R. / Kerff, F. / Dobson, C.M. / Dumoulin, M.
History
DepositionOct 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 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)14,9804
Polymers14,6921
Non-polymers2883
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-26 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.773, 56.655, 60.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14691.678 Da / Num. of mol.: 1 / Mutation: W64R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Production host: Komagataella pastoris (fungus) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.86 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.25M (NH4)2SO4, 0.1M cacodylate pH 6.5, 10 mM Tris pH 7, 14.4 TP buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980119943619 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980119943619 Å / Relative weight: 1
ReflectionResolution: 1.15→41.384 Å / Num. obs: 39372 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.35 % / Biso Wilson estimate: 12.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.04
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.15-1.220.7691.7560790.798195.1
1.22-1.30.5782.5759220.887199.1
1.3-1.410.4293.6755480.929199.3
1.41-1.540.276.0651540.968199.7
1.54-1.720.16410.7546870.984199.7
1.72-1.990.10416.3541460.992199.5
1.99-2.430.07221.9335390.995199.4
2.43-3.430.05926.627700.997199
3.43-41.3840.05330.0716400.996199.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å41.38 Å
Translation2.5 Å41.38 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.4.0phasing
PHENIX1.1refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSF

1jsf


Resolution: 1.15→30.298 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.1927 1973 5.01 %
Rwork0.1606 --
obs0.1623 39365 98.7 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Bsol: 45.093 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso max: 47.65 Å2 / Biso mean: 16.58 Å2 / Biso min: 6.28 Å2
Baniso -1Baniso -2Baniso -3
1-4.6074 Å2-0 Å2-0 Å2
2---2.6095 Å2-0 Å2
3----1.9979 Å2
Refinement stepCycle: final / Resolution: 1.15→30.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 15 164 1205
Biso mean--26.14 27.25 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221126
X-RAY DIFFRACTIONf_angle_d1.9821526
X-RAY DIFFRACTIONf_chiral_restr0.121158
X-RAY DIFFRACTIONf_plane_restr0.012200
X-RAY DIFFRACTIONf_dihedral_angle_d12.409429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.17640.35641280.33572395X-RAY DIFFRACTION90
1.1764-1.20820.34281370.30322619X-RAY DIFFRACTION99
1.2082-1.24380.25321320.25512658X-RAY DIFFRACTION99
1.2438-1.28390.24661430.2282638X-RAY DIFFRACTION99
1.2839-1.32980.24251390.19912666X-RAY DIFFRACTION99
1.3298-1.3830.22791440.18542662X-RAY DIFFRACTION99
1.383-1.4460.20481330.17242668X-RAY DIFFRACTION99
1.446-1.52220.22551500.14212671X-RAY DIFFRACTION100
1.5222-1.61760.19881470.13652680X-RAY DIFFRACTION100
1.6176-1.74250.17881340.12882699X-RAY DIFFRACTION100
1.7425-1.91780.15821500.1312678X-RAY DIFFRACTION100
1.9178-2.19520.18731390.13412728X-RAY DIFFRACTION99
2.1952-2.76540.16361450.13432737X-RAY DIFFRACTION99
2.7654-30.2980.17841520.16862893X-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://pdbjlvh1.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