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- PDB-6jxp: Room temperature structure of lysozyme delivered in LCP by serial... -

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Basic information

Entry
Database: PDB / ID: 6jxp
TitleRoom temperature structure of lysozyme delivered in LCP by serial millisecond crystallography
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / serial crystallography / LCP
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
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: Sample delivery using viscous media, a syringe and a syringe pump for serial crystallography.
Authors: Park, S.Y. / Nam, K.H.
History
DepositionApr 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.2Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_R_split
Revision 1.3Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.4Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3293
Polymers16,2581
Non-polymers712
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.410, 78.410, 37.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-349-

HOH

31A-388-

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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 293.5 K / Method: small tubes / Details: sodium acetate, PEG 8000, NaCl

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.56→78.7 Å / Num. obs: 17418 / % possible obs: 99.93 % / Redundancy: 318.4 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.991 / R split: 0.0987 / Net I/σ(I): 6
Reflection shellResolution: 1.56→1.61 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 1685 / CC1/2: 0.436 / R split: 0.8866 / % possible all: 99.23
Serial crystallography sample deliveryMethod: injection
Serial crystallography data reductionCrystal hits: 24258 / Frames indexed: 19411 / Frames total: 40000 / Lattices indexed: 19411

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IRJ
Resolution: 1.56→55.44 Å / SU ML: 0.1805 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7775
RfactorNum. reflection% reflection
Rfree0.2003 1738 10.01 %
Rwork0.1675 --
obs0.1708 17361 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.94 Å2
Refinement stepCycle: LAST / Resolution: 1.56→55.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 88 1091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021042
X-RAY DIFFRACTIONf_angle_d1.02221416
X-RAY DIFFRACTIONf_chiral_restr0.0609147
X-RAY DIFFRACTIONf_plane_restr0.0055186
X-RAY DIFFRACTIONf_dihedral_angle_d12.1477622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.610.35041400.35381270X-RAY DIFFRACTION98.95
1.61-1.660.3141420.25441270X-RAY DIFFRACTION100
1.66-1.720.28871410.24211271X-RAY DIFFRACTION100
1.72-1.790.25371440.21041273X-RAY DIFFRACTION99.16
1.79-1.870.24541410.19481281X-RAY DIFFRACTION100
1.87-1.970.20121430.16371281X-RAY DIFFRACTION100
1.97-2.090.19491440.15241297X-RAY DIFFRACTION100
2.09-2.250.19281440.15841297X-RAY DIFFRACTION100
2.25-2.480.18651450.15231303X-RAY DIFFRACTION100
2.48-2.830.19141450.15881313X-RAY DIFFRACTION100
2.83-3.570.18081490.1721338X-RAY DIFFRACTION100
3.57-55.480.18941600.1491429X-RAY DIFFRACTION100

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