[English] 日本語
Yorodumi
- PDB-7bdz: X-ray structure of Hen Egg White Lysozyme with dirhodium tetraace... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bdz
TitleX-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (1)
ComponentsLysozyme
KeywordsHYDROLASE / Metallodrug / Metal/protein adduct / bimetallic compounds
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 / Rhodium / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLoreto, D. / Merlino, A. / Ferraro, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research22587 Italy
CitationJournal: Int J Mol Sci / Year: 2021
Title: Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme.
Authors: Loreto, D. / Ferraro, G. / Merlino, A.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,83823
Polymers14,3311
Non-polymers1,50722
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint13 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.964, 77.964, 37.291
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-351-

HOH

21AAA-414-

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, lysozyme

-
Non-polymers , 5 types, 147 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-RH / Rhodium


Mass: 102.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→25.48 Å / Num. obs: 8895 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.045 / Net I/σ(I): 14.9
Reflection shellResolution: 1.94→1.97 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 426 / CC1/2: 0.808 / Rpim(I) all: 0.249

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193l

193l


Resolution: 1.94→25.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.66 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2174 430 4.845 %
Rwork0.1562 8445 -
all0.159 --
obs-8875 99.162 %
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: 21.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.299 Å20 Å20 Å2
2---0.299 Å20 Å2
3---0.598 Å2
Refinement stepCycle: LAST / Resolution: 1.94→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 76 126 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131097
X-RAY DIFFRACTIONr_bond_other_d0.0020.018943
X-RAY DIFFRACTIONr_ext_dist_refined_d0.130.019
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.7051476
X-RAY DIFFRACTIONr_angle_other_deg1.511.5852171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3420.95263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03915168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3441511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2240.2266
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.2928
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2526
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.231
X-RAY DIFFRACTIONr_nbd_other0.3090.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.250
X-RAY DIFFRACTIONr_mcbond_it1.5761.959532
X-RAY DIFFRACTIONr_mcbond_other1.4431.934524
X-RAY DIFFRACTIONr_mcangle_it2.0882.903659
X-RAY DIFFRACTIONr_mcangle_other2.0852.904659
X-RAY DIFFRACTIONr_scbond_it2.5262.333564
X-RAY DIFFRACTIONr_scbond_other2.5242.332565
X-RAY DIFFRACTIONr_scangle_it3.8963.401826
X-RAY DIFFRACTIONr_scangle_other3.8943.401827
X-RAY DIFFRACTIONr_lrange_it5.88624.4271318
X-RAY DIFFRACTIONr_lrange_other5.88424.4331319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.243340.208593X-RAY DIFFRACTION98.1221
1.99-2.0450.198370.173597X-RAY DIFFRACTION100
2.045-2.1040.244260.163583X-RAY DIFFRACTION100
2.104-2.1690.261210.16571X-RAY DIFFRACTION100
2.169-2.240.177240.145549X-RAY DIFFRACTION100
2.318-2.4060.238280.142519X-RAY DIFFRACTION99.8175
2.406-2.5040.234200.157505X-RAY DIFFRACTION100
2.504-2.6150.187250.155477X-RAY DIFFRACTION100
2.615-2.7420.234190.147452X-RAY DIFFRACTION99.5772
2.742-2.890.253190.145453X-RAY DIFFRACTION99.5781
2.89-3.0650.243250.14409X-RAY DIFFRACTION100
3.065-3.2760.18240.122383X-RAY DIFFRACTION98.7864
3.537-3.8730.17210.138338X-RAY DIFFRACTION98.6264
3.873-4.3270.172220.143309X-RAY DIFFRACTION98.5119
4.327-4.9920.311180.175266X-RAY DIFFRACTION97.931
6.101-8.5760.229100.218187X-RAY DIFFRACTION95.6311

+
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