[English] 日本語
Yorodumi
- PDB-1gd6: STRUCTURE OF THE BOMBYX MORI LYSOZYME -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gd6
TitleSTRUCTURE OF THE BOMBYX MORI LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE / BMLZ
Function / homology
Function and homology information


lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.5 Å
AuthorsMatsuura, A. / Aizawa, T. / Yao, M. / Kawano, K. / Tanaka, I. / Nitta, K.
CitationJournal: Biochemistry / Year: 2002
Title: Structural analysis of an insect lysozyme exhibiting catalytic efficiency at low temperatures.
Authors: Matsuura, A. / Yao, M. / Aizawa, T. / Koganesawa, N. / Masaki, K. / Miyazawa, M. / Demura, M. / Tanaka, I. / Kawano, K. / Nitta, K.
History
DepositionSep 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)13,7781
Polymers13,7781
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.268, 77.268, 72.925
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer

-
Components

#1: Protein LYSOZYME


Mass: 13777.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Pichia pastoris (fungus) / References: UniProt: P48816, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.957779 Å3/Da / Density % sol: 68.9623903 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 69 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium sulfate1drop
326 %(w/v)PEG80001drop
40.1 Msodium cacodylate1reservoir

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Aug 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 55985 / Num. obs: 7862 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 7.12 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.8388 / Num. unique all: 742 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 97639
Reflection shell
*PLUS
% possible obs: 96.4 % / Redundancy: 5.08 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.84

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: molecular replacement / Resolution: 2.5→10 Å / Isotropic thermal model: RESTRAINTS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 747 9.4 %RAMDOM
Rwork0.1809 ---
all-7917 --
obs-7685 97.1 %-
Solvent computationBsol: 30.2625 Å2 / ksol: 0.358547 e/Å3
Displacement parametersBiso mean: 38.84 Å2
Baniso -1Baniso -2Baniso -3
1-5.068 Å20 Å20 Å2
2--5.068 Å20 Å2
3----10.136 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.322 Å0.27 Å
Luzzati sigma a0.51 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 64 1027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008512
X-RAY DIFFRACTIONc_angle_deg1.55289
X-RAY DIFFRACTIONc_torsion_deg23.47519
X-RAY DIFFRACTIONc_torsion_impr_deg0.73009
X-RAY DIFFRACTIONc_dihedral_angle_d23.47519
X-RAY DIFFRACTIONc_improper_angle_d0.73009
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.3059 -
Rwork0.3019 550
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.223 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.47519
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73009

+
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