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- PDB-6q88: RT structure of HEWL at 5 kGy -

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Basic information

Entry
Database: PDB / ID: 6q88
TitleRT structure of HEWL at 5 kGy
ComponentsLysozyme C
KeywordsHYDROLASE / Antimicrobial / low-dose / serial crystallography
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
DI(HYDROXYETHYL)ETHER / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74007062403 Å
Authorsde la Mora, E. / Coquelle, N. / Bury, C.S. / Rosenthal, M. / Garman, E.F. / Burghammer, M. / Colletier, J.P. / Weik, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.
Authors: de la Mora, E. / Coquelle, N. / Bury, C.S. / Rosenthal, M. / Holton, J.M. / Carmichael, I. / Garman, E.F. / Burghammer, M. / Colletier, J.P. / Weik, M.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 26, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4733
Polymers14,3311
Non-polymers1422
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-5 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 38.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4
Details: 20 % NaCl 6 % PEG 6000 150 mM ammonium acetate pH 4.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9219 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9219 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 13310 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 195.8 % / Biso Wilson estimate: 26.1412275865 Å2 / Net I/σ(I): 7.14
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 106.9 % / Num. unique obs: 802 / R split: 0.4816 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YDG

2ydg


Resolution: 1.74007062403→19.8250007625 Å / SU ML: 0.209005576276 / Cross valid method: FREE R-VALUE / σ(F): 1.35052863581 / Phase error: 20.2404594086
RfactorNum. reflection% reflection
Rfree0.199444567544 869 6.67691125624 %
Rwork0.175272196531 --
obs0.176936877007 13015 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.5473547044 Å2
Refinement stepCycle: LAST / Resolution: 1.74007062403→19.8250007625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 89 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005111130479291065
X-RAY DIFFRACTIONf_angle_d0.7650278643091443
X-RAY DIFFRACTIONf_chiral_restr0.0859671389367148
X-RAY DIFFRACTIONf_plane_restr0.00415923807767189
X-RAY DIFFRACTIONf_dihedral_angle_d15.0330569293403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7401-1.8490.3066390315271400.2910913608921965X-RAY DIFFRACTION100
1.849-1.99170.2292205167711420.1875911056511987X-RAY DIFFRACTION100
1.9917-2.19190.2021391489381430.1654410021181994X-RAY DIFFRACTION100
2.1919-2.50850.19246421051440.1750315853492013X-RAY DIFFRACTION100
2.5085-3.15840.2048481476991460.1898557278192034X-RAY DIFFRACTION100
3.1584-19.82630.1833037124391540.1571596931032153X-RAY DIFFRACTION100

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