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- PDB-8y1r: in situ room temperature Laue crystallography -

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Basic information

Entry
Database: PDB / ID: 8y1r
Titlein situ room temperature Laue crystallography
ComponentsLysozyme C
KeywordsLYASE / Complex
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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z.J. / Wang, S.S. / Pan, Q.Y. / Yu, L. / Su, Z.H. / Yang, T.Y. / Wang, Y.Z. / Zhang, W.Z. / Hao, Q. / Gao, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: To Be Published
Title: BL03HB: Laue crystallography beamline at SSRF
Authors: Wang, Z.J. / Wang, S.S. / Pan, Q.Y. / Yu, L. / Su, Z.H. / Yang, T.Y. / Wang, Y.Z. / Zhang, W.Z. / Wang, Q.S. / Hao, Q. / Gao, X.Y.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.560, 78.560, 37.560
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-207-

HOH

21A-252-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 293 K / Method: evaporation
Details: sodium acetate buffer, pH 4.55, and sodium chloride

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: 20 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL03HB / Wavelength: 0.6 - 1.58
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
21.581
ReflectionResolution: 2→21.48 Å / Num. obs: 7617 / % possible obs: 90.83 % / Redundancy: 1 % / CC1/2: 0.92 / Rmerge(I) obs: 0.24 / Net I/av σ(I): 5 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.15 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4 / Num. unique obs: 1284 / CC1/2: 0.91 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
LaueViewdata reduction
LaueViewdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EPE

2epe


Resolution: 2→21.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 759 9.98 %
Rwork0.2008 --
obs0.2068 7606 90.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→21.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 73 1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081021
X-RAY DIFFRACTIONf_angle_d1.1281381
X-RAY DIFFRACTIONf_dihedral_angle_d15.463365
X-RAY DIFFRACTIONf_chiral_restr0.048144
X-RAY DIFFRACTIONf_plane_restr0.007181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.29811420.23721284X-RAY DIFFRACTION88
2.15-2.370.25371520.19711374X-RAY DIFFRACTION92
2.37-2.710.23641540.20121384X-RAY DIFFRACTION93
2.71-3.410.28481560.20171411X-RAY DIFFRACTION94
3.42-21.480.2451550.19011394X-RAY DIFFRACTION87

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