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- PDB-7cdm: Lysozyme room-temperature structure determined by SS-ROX combined... -

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Basic information

Entry
Database: PDB / ID: 7cdm
TitleLysozyme room-temperature structure determined by SS-ROX combined with HAG method, 42 kGy (4500 images from 2nd half of data set)
ComponentsLysozyme C
KeywordsHYDROLASE / Chicken egg white / antimicrobial enzyme / N-acetylmuramide glycanhydrolase / lysozyme-like fold
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
MALONATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05783 Japan
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method.
Authors: Hasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T.
History
DepositionJun 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4563
Polymers14,3311
Non-polymers1252
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.382, 78.382, 38.763
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-317-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 293 K / Method: batch mode
Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was ...Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was stopped by adding 2.4 M Na-Malonate pH 3.1, 3.6 % w/v PEG6000.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→55.42 Å / Num. obs: 13831 / % possible obs: 100 % / Redundancy: 188.6 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.9766 / Net I/σ(I): 5.99
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 664 / CC1/2: 0.5981
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.17.1_3660refinement
CrystFEL0.8.0data reduction
CrystFEL0.7.0data scaling
Cootmodel building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4eta

4eta


Resolution: 1.7→55.42 Å / SU ML: 0.1808 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 704 5.1 %
Rwork0.1871 13098 -
obs0.1886 13802 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 49 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541027
X-RAY DIFFRACTIONf_angle_d0.73681388
X-RAY DIFFRACTIONf_chiral_restr0.0497144
X-RAY DIFFRACTIONf_plane_restr0.0033183
X-RAY DIFFRACTIONf_dihedral_angle_d13.0014367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.31011220.25812575X-RAY DIFFRACTION100
1.83-2.020.23681300.19642576X-RAY DIFFRACTION100
2.02-2.310.19451480.17142580X-RAY DIFFRACTION100
2.31-2.910.22021520.17632607X-RAY DIFFRACTION100
2.91-55.420.19581520.18272760X-RAY DIFFRACTION100

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