[English] 日本語
Yorodumi
- PDB-30jy: X-ray structure of lysozyme treated with V(V)-lactate complex (st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30jy
TitleX-ray structure of lysozyme treated with V(V)-lactate complex (structure D)
ComponentsLysozyme C
KeywordsHYDROLASE / protein metalation
Function / homology
Function and homology information


Lactose synthesis / 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 bacterium ...Lactose synthesis / 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 bacterium / defense response to Gram-positive bacterium / Golgi apparatus / endoplasmic reticulum / : / 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
: / oxovanadium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsPaolillo, M. / Ferraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022JMFC3X Italy
CitationJournal: Inorg.Chem. / Year: 2026
Title: Speciation, Protein Binding, Biotransformation, and Cytotoxicity of a VV-Lactate Complex.
Authors: Paolillo, M. / Cuomo, V. / Ferraro, G. / Imbimbo, P. / Gumerova, N.I. / Pisanu, F. / Garribba, E. / Rompel, A. / Merlino, A.
History
DepositionApr 29, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1676
Polymers14,3311
Non-polymers8365
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-6 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.405, 76.405, 36.976
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-329-

HOH

21AAA-337-

HOH

31AAA-350-

HOH

41AAA-459-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

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


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

-
Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-A1J62 / Trinuclear vanadium-lactate complex


Mass: 440.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O13V3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M sodium formate, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.23→54.03 Å / Num. obs: 30853 / % possible obs: 95.3 % / Redundancy: 8.9 % / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 1.23→1.25 Å / Num. unique obs: 1100 / CC1/2: 0.331

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→54.026 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.897 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2177 1468 4.918 %
Rwork0.1797 28383 -
all0.181 --
obs-29851 92.269 %
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: 17.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.029 Å20 Å20 Å2
2---0.029 Å20 Å2
3---0.058 Å2
Refinement stepCycle: LAST / Resolution: 1.23→54.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 42 160 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121090
X-RAY DIFFRACTIONr_bond_other_d0.0010.014985
X-RAY DIFFRACTIONr_angle_refined_deg4.1711.7181485
X-RAY DIFFRACTIONr_angle_other_deg1.6461.5952250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17520.46964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5361512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2430.2249
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2971
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2527
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2770.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.222
X-RAY DIFFRACTIONr_nbd_other0.2390.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_mcbond_it1.7051.494519
X-RAY DIFFRACTIONr_mcbond_other1.7021.494519
X-RAY DIFFRACTIONr_mcangle_it2.4692.253650
X-RAY DIFFRACTIONr_mcangle_other2.4712.256651
X-RAY DIFFRACTIONr_scbond_it2.6531.901570
X-RAY DIFFRACTIONr_scbond_other2.6421.845541
X-RAY DIFFRACTIONr_scangle_it4.1442.749832
X-RAY DIFFRACTIONr_scangle_other4.1392.654792
X-RAY DIFFRACTIONr_lrange_it5.83819.8581322
X-RAY DIFFRACTIONr_lrange_other5.62418.9251277
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
1.23-1.2620.311620.28110300.28323150.8230.84347.17060.279
1.262-1.2960.316820.27515220.27723010.8280.83969.70880.269
1.296-1.3340.284790.2517520.25122310.8680.88682.07080.241
1.334-1.3750.2821040.24119310.24321690.8920.89393.8220.225
1.375-1.420.2661170.22919770.23121220.9020.9198.68050.206
1.42-1.470.234960.21319270.21420280.9310.93599.75340.195
1.47-1.5250.232870.19818800.19919670.9160.9391000.184
1.525-1.5880.2421070.20417960.20719030.9280.9341000.192
1.588-1.6580.249940.1917320.19318260.9340.9481000.181
1.658-1.7390.218920.18616580.18717500.9450.9511000.18
1.739-1.8330.239790.18515870.18716660.9260.9471000.185
1.833-1.9440.223680.18215180.18415860.9390.9521000.188
1.944-2.0780.206830.17214160.17414990.9570.9611000.188
2.078-2.2440.204810.15913090.16213900.9510.9631000.18
2.244-2.4580.169550.15512450.15513000.9690.9691000.183
2.458-2.7480.21450.16311250.16411700.9550.9671000.198
2.748-3.1710.19510.17410010.17510530.9520.96399.9050.22
3.171-3.8810.142330.1458730.1459060.9760.9771000.184
3.881-5.4740.222310.166890.1627240.9560.97299.44750.22
5.474-54.0260.319220.2354130.2394400.9090.9498.86360.348

+
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