[English] 日本語
Yorodumi
- PDB-7c09: Structure of lysozyme obtained in SSRF using serial crystallography -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c09
TitleStructure of lysozyme obtained in SSRF using serial crystallography
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhao, F.Z.
CitationJournal: Lab Chip / Year: 2020
Title: A novel sample delivery system based on circular motion for in situ serial synchrotron crystallography.
Authors: Zhao, F.Z. / Sun, B. / Yu, L. / Xiao, Q.J. / Wang, Z.J. / Chen, L.L. / Liang, H. / Wang, Q.S. / He, J.H. / Yin, D.C.
History
DepositionApr 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
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)78.000, 78.000, 38.000
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
11A-235-

HOH

-
Components

#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
#2: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: microbatch / Details: NaCl

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→27.58 Å / Num. obs: 6326 / % possible obs: 99.89 % / Redundancy: 11.97 % / R split: 0.209 / Net I/σ(I): 4.5
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1131 / R split: 0.4796
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
CrystFEL8data scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 2.2→27.577 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2277 632 9.99 %
Rwork0.1778 --
obs0.1828 6326 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.42 Å2 / Biso mean: 72.3896 Å2 / Biso min: 52.43 Å2
Refinement stepCycle: final / Resolution: 2.2→27.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 0 64 1064
Biso mean---79.21 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2003-2.37010.28281230.21591110
2.3701-2.60840.28531240.21381111
2.6084-2.98550.27421230.20551115
2.9855-3.75990.25591270.1831139
3.7599-27.5770.20091350.16551219
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12390.03320.30750.07740.00150.1014-0.03660.347-0.4303-0.23-0.09760.08780.9907-0.368100.7619-0.021-0.02670.6277-0.00670.6734-6.711516.1589.5573
20.2146-0.11990.08750.092-0.24060.19980.1008-0.4844-0.0661-0.1249-0.13170.51830.50980.2854-00.6694-0.00730.02990.6783-0.02960.7908-11.671723.620520.453
30.0883-0.00310.1007-0.1834-0.1595-0.01460.1058-0.2221-0.0996-0.23960.1444-0.1932-0.01760.195300.5720.00120.00710.6673-0.00040.62880.370321.516212.8907
4-0.02370.07050.03940.01950.0604-0.0047-0.38560.6110.2550.0434-0.638-0.2765-0.58160.781900.7725-0.0035-0.06050.77990.00390.692714.535919.69923.9746
5-0.04190.01240.0895-0.0129-0.1011-0.0656-0.34520.04420.45010.44040.1003-0.25380.4349-0.418300.71390.0239-0.07490.69750.00730.54865.575317.512520.5555
60.0771-0.074-0.07780.1420.02530.389-0.0081-0.42920.10250.15160.07260.17840.23340.086300.70190.0601-0.04340.7599-0.03820.6886.503415.144731.2821
70.1997-0.07230.1132-0.0620.01170.0999-0.2102-0.0022-0.30660.11880.20710.10730.15660.00600.65860.03130.02480.65580.02380.6731-2.069213.555622.2903
8-0.1-0.03560.0024-0.04680.09430.015-0.7228-0.19590.92640.15840.5492-0.03641.18810.763700.68680.13440.00560.7335-0.08620.7275-2.254427.413726.1795
90.0230.0284-0.03430.0503-0.03020.05010.4794-1.54540.686-0.1774-0.02250.1986-0.36630.416200.6975-0.10530.14770.8966-0.13680.782.779331.460617.7028
100.01580.20140.0021-0.1399-0.01940.15530.0685-0.0650.3788-0.2581-0.16440.1753-0.19-0.5674-00.68990.0393-0.06280.7379-0.00920.7443-8.383728.34448.0576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )A15 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )A25 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )A43 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 58 )A51 - 58
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 78 )A59 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 99 )A79 - 99
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 108 )A100 - 108
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 114 )A109 - 114
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 129 )A115 - 129

+
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