[English] 日本語
Yorodumi
- PDB-8aj5: X-ray structure of lysozyme obtained upon reaction with [VIVO(mal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aj5
TitleX-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (Structure B)
ComponentsLysozyme
KeywordsHYDROLASE / metallodrug / vanadium / oxidovanadium / covalent binding / non-covalent binding / protein-metal interaction
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / 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 / VANADATE ION / bis(oxidanyl)vanadium / oxovanadium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsPaolillo, M. / Merlino, A. / Ferraro, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Inorg.Chem. / Year: 2022
Title: Multiple and Variable Binding of Pharmacologically Active Bis(maltolato)oxidovanadium(IV) to Lysozyme.
Authors: Ferraro, G. / Paolillo, M. / Sciortino, G. / Garribba, E. / Merlino, A.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: 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
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,46517
Polymers14,3311
Non-polymers1,13416
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.230, 78.230, 37.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-206-

VVB

21AAA-206-

VVB

31AAA-330-

HOH

41AAA-352-

HOH

51AAA-385-

HOH

61AAA-415-

HOH

71AAA-430-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698

-
Non-polymers , 7 types, 148 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VVB / bis(oxidanyl)vanadium


Mass: 84.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2V / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→55.32 Å / Num. obs: 28122 / % possible obs: 98.9 % / Redundancy: 20 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 14.3
Reflection shellResolution: 1.31→1.33 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 25.8 / Num. unique obs: 28122 / CC1/2: 0.755 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193l

193l


Resolution: 1.31→55.317 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.926 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1976 1403 4.999 %
Rwork0.1676 26662 -
all0.169 --
obs-28065 98.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.037 Å2-0 Å2-0 Å2
2--0.037 Å2-0 Å2
3----0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.31→55.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 61 132 1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141032
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6251560
X-RAY DIFFRACTIONr_angle_other_deg1.581.5992351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26619.86172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7451515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02318
X-RAY DIFFRACTIONr_nbd_refined0.2760.2298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2950
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2543
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.213
X-RAY DIFFRACTIONr_nbd_other0.270.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1190.21
X-RAY DIFFRACTIONr_mcbond_it1.671.61556
X-RAY DIFFRACTIONr_mcbond_other1.6161.6553
X-RAY DIFFRACTIONr_mcangle_it2.3892.415703
X-RAY DIFFRACTIONr_mcangle_other2.392.419704
X-RAY DIFFRACTIONr_scbond_it2.9052.097602
X-RAY DIFFRACTIONr_scbond_other2.7872.017579
X-RAY DIFFRACTIONr_scangle_it4.2642.942857
X-RAY DIFFRACTIONr_scangle_other4.1312.857834
X-RAY DIFFRACTIONr_lrange_it6.64921.3911428
X-RAY DIFFRACTIONr_lrange_other6.64821.4171429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.31-1.3440.2661090.26118730.26220620.8880.87396.12030.248
1.344-1.3810.2381090.24518380.24420110.9030.89796.81750.222
1.381-1.4210.232890.22718660.22719770.9080.9298.88720.2
1.421-1.4650.239850.21817600.21918730.9220.92698.50510.191
1.465-1.5130.212970.19317090.19418450.9410.93797.88620.171
1.513-1.5660.204740.19516910.19617970.9410.93998.21930.171
1.566-1.6250.207790.18216290.18417320.9390.95198.61430.161
1.625-1.6910.231800.1715700.17216610.9330.95699.33780.152
1.691-1.7660.203850.16515050.16715970.9430.95999.56170.153
1.766-1.8520.173830.16114520.16215470.9590.96399.22430.152
1.852-1.9520.197750.15613670.15814530.9580.96799.24290.153
1.952-2.070.227680.1513210.15413990.9480.96799.28520.15
2.07-2.2130.21600.14612480.14913110.9550.9799.77120.155
2.213-2.390.145640.1411500.14112160.9750.97399.83550.152
2.39-2.6180.2560.14910820.15111380.9580.9721000.168
2.618-2.9260.183500.1489920.1510420.9650.971000.175
2.926-3.3770.191500.1558770.1579270.9610.9691000.191
3.377-4.1320.165420.157570.1517990.9710.9731000.193
4.132-5.8280.185310.1555940.1576250.9770.9791000.214
5.828-55.3170.289170.2713730.2723920.9550.92299.48980.374

+
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