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- PDB-7d04: Lysozyme structure SS3 from SS mode -

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Basic information

Entry
Database: PDB / ID: 7d04
TitleLysozyme structure SS3 from SS mode
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / XFEL / SFX / SElf-seeded mode
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKang, H.S. / Lee, S.J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1A2B4007274 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1F1A1075828 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A6B4023605 Korea, Republic Of
CitationJournal: Nat Photonics / Year: 2021
Title: High-brightness self-seeded X-ray free-electron laser covering the 3.5 keV to 14.6 keV range
Authors: Nam, I. / Min, C.K. / Oh, B. / Kim, G. / Na, D. / Suh, Y.J. / Yang, H. / Cho, M.H. / Kim, C. / Kim, M.J. / Shim, C.H. / Ko, J.H. / Heo, H. / Park, J. / Kim, J. / Park, S. / Park, G. / Kim, S. ...Authors: Nam, I. / Min, C.K. / Oh, B. / Kim, G. / Na, D. / Suh, Y.J. / Yang, H. / Cho, M.H. / Kim, C. / Kim, M.J. / Shim, C.H. / Ko, J.H. / Heo, H. / Park, J. / Kim, J. / Park, S. / Park, G. / Kim, S. / Chun, S.H. / Hyun, H. / Lee, J.H. / Kim, K.S. / Eom, I. / Rah, S. / Shu, D. / Kim, K.J. / Terentyev, S. / Blank, V. / Shvydko, Y. / Lee, S.J. / Kang, H.S.
History
DepositionSep 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)16,2581
Polymers16,2581
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6480 Å2
Unit cell
Length a, b, c (Å)78.895, 78.895, 37.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-238-

HOH

31A-272-

HOH

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Components

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


Mass: 16257.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 32.03 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: batch mode
Details: 100 mM sodium acetate (pH 4.0), 6% (w/v) polyethylene glycol 8,000, and 3.5 M NaCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.7→27.89 Å / Num. obs: 25173 / % possible obs: 100 % / Redundancy: 140.6 % / CC star: 0.964 / R split: 0.295 / Net I/σ(I): 3.52
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2532 / CC star: 0.869 / R split: 0.647
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
CrystFELV0.9.1data reduction
CrystFELV0.9.1data scaling
PHENIXV1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDS

1vds


Resolution: 1.7→27.89 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1249 4.97 %
Rwork0.213 --
obs0.2147 25111 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 72 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071021
X-RAY DIFFRACTIONf_angle_d1.051381
X-RAY DIFFRACTIONf_dihedral_angle_d15.511143
X-RAY DIFFRACTIONf_chiral_restr0.059144
X-RAY DIFFRACTIONf_plane_restr0.009181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.31641400.26262670X-RAY DIFFRACTION100
1.77-1.850.32461400.24372643X-RAY DIFFRACTION100
1.85-1.950.22781390.21132649X-RAY DIFFRACTION100
1.95-2.070.23611430.18752656X-RAY DIFFRACTION100
2.07-2.230.25531410.18852648X-RAY DIFFRACTION100
2.23-2.450.21451310.19072639X-RAY DIFFRACTION100
2.45-2.810.24241440.20792658X-RAY DIFFRACTION100
2.81-3.530.22571330.21382650X-RAY DIFFRACTION100
3.54-27.890.26361380.2292649X-RAY DIFFRACTION100

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