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- PDB-8b3t: Hen Egg White Lysozyme 4s in situ crystallization -

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Basic information

Entry
Database: PDB / ID: 8b3t
TitleHen Egg White Lysozyme 4s in situ crystallization
ComponentsLysozyme
KeywordsHYDROLASE
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHenkel, A. / Galchenkova, M. / Yefanov, O. / Hakanpaeae, J. / Chapman, H.N. / Oberthuer, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Iucrj / Year: 2023
Title: JINXED: just in time crystallization for easy structure determination of biological macromolecules.
Authors: Henkel, A. / Galchenkova, M. / Maracke, J. / Yefanov, O. / Klopprogge, B. / Hakanpaa, J. / Mesters, J.R. / Chapman, H.N. / Oberthuer, D.
#1: Journal: Biorxiv / Year: 2022
Title: JINXED: Just in time crystallization for easy structure determination of biological macromolecules
Authors: Henkel, A. / Galchenkova, M. / Maracke, J. / Yefanov, O. / Hakanpaa, J. / Mesters, J.R. / Chapman, H.N. / Oberthur, D.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Revision 1.2May 17, 2023Group: 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 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7329
Polymers14,3311
Non-polymers4018
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-22 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.200, 79.200, 37.800
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
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-360-

HOH

31A-372-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P00698

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Non-polymers , 5 types, 80 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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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Details

Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: microfluidic
Details: 0.1 M sodium acetate, pH 4.6, 2.7 M NaCl, 15 % PEG4000, 6 % ethylene glycol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.78→39.6 Å / Num. obs: 12126 / % possible obs: 100 % / Redundancy: 408.01 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.992 / CC star: 0.998 / R split: 0.1022 / Net I/σ(I): 10.76
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 54.7 % / Num. unique obs: 601 / CC1/2: 0.275 / CC star: 0.656 / R split: 1.46 / % possible all: 100
Serial crystallography sample deliveryDescription: CFEL TapeDrive 2.0 / Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FTR

6ftr


Resolution: 1.78→39.6 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 1181 10.02 %
Rwork0.1635 10600 -
obs0.1671 11781 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.99 Å2
Refinement stepCycle: LAST / Resolution: 1.78→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 23 72 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571188
X-RAY DIFFRACTIONf_angle_d0.80031613
X-RAY DIFFRACTIONf_chiral_restr0.0472160
X-RAY DIFFRACTIONf_plane_restr0.0074222
X-RAY DIFFRACTIONf_dihedral_angle_d6.087181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.39831250.3631105X-RAY DIFFRACTION84.19
1.86-1.960.31421470.28511318X-RAY DIFFRACTION99.32
1.96-2.080.25271480.20361332X-RAY DIFFRACTION99.93
2.08-2.240.21441470.17191328X-RAY DIFFRACTION100
2.24-2.470.18781490.13811334X-RAY DIFFRACTION100
2.47-2.830.1771500.13931352X-RAY DIFFRACTION100
2.83-3.560.17461520.14231371X-RAY DIFFRACTION100
3.56-39.60.17511630.14191460X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 0.74015624002 Å / Origin y: 99.8985912215 Å / Origin z: 9.10467614976 Å
111213212223313233
T0.134863624435 Å2-0.00494931138808 Å2-0.00134068249905 Å2-0.150111167277 Å20.0159248695456 Å2--0.146061129108 Å2
L1.01855968649 °20.505558969408 °2-0.0822106934661 °2-1.31184663153 °2-0.240768355681 °2--0.895055327728 °2
S-0.019882616538 Å °-0.00907520477368 Å °-0.0161192964446 Å °-0.0325782306703 Å °0.0236357107665 Å °-0.0666792898046 Å °0.0597570049165 Å °0.0193313311693 Å °0.00047535548559 Å °
Refinement TLS groupSelection details: all

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