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- PDB-8a9d: Multicrystal room temperature structure of Lysozyme collected usi... -

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Basic information

Entry
Database: PDB / ID: 8a9d
TitleMulticrystal room temperature structure of Lysozyme collected using a double multilayer monochromator.
ComponentsLysozyme
KeywordsHYDROLASE / Lysozyme / Multi-crystal / DMM / Multilayer mmonochromator
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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: 2.1 Å
AuthorsSandy, J. / Cheruvara, H. / Mikolajek, H. / Sanchez-Weatherby, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,3542
Polymers14,3311
Non-polymers231
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6460 Å2
Unit cell
Length a, b, c (Å)78.485, 78.485, 38.139
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-338-

HOH

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 21

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0539.97
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2932lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2933lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2934lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2935lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2936lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2937lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2938lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2939lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29310lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29311lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29312lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29313lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29314lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29315lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29316lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29317lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29318lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29319lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29320lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
29321lipidic cubic phase4.51M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 9, 2022
RadiationMonochromator: Double multilayer monochromator (DMM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.1→78.49 Å / Num. obs: 7390 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 29.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.524 / Rpim(I) all: 0.137 / Rrim(I) all: 0.543 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 15.99 % / Rmerge(I) obs: 3.26 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 371 / CC1/2: 0.299 / Rpim(I) all: 0.834 / Rrim(I) all: 3.369 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LYZ

2lyz


Resolution: 2.1→55.5 Å / SU ML: 0.262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 735 10 %
Rwork0.1935 6614 -
obs0.199 7349 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 1 72 1050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151003
X-RAY DIFFRACTIONf_angle_d0.36121361
X-RAY DIFFRACTIONf_chiral_restr0.0372145
X-RAY DIFFRACTIONf_plane_restr0.0037178
X-RAY DIFFRACTIONf_dihedral_angle_d4.3548142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.33481420.27961279X-RAY DIFFRACTION99.58
2.26-2.490.3061440.24981295X-RAY DIFFRACTION99.86
2.49-2.850.26781450.23121298X-RAY DIFFRACTION99.93
2.85-3.590.25341470.18351326X-RAY DIFFRACTION99.8
3.59-55.50.20521570.15391416X-RAY DIFFRACTION99.94

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