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- PDB-9fa5: Lysozyme structure at room temperature by serial synchrotron crys... -

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Basic information

Entry
Database: PDB / ID: 9fa5
TitleLysozyme structure at room temperature by serial synchrotron crystallography with COC chips
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / Serial synchrotron crystallography / Fixed target
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
DI(HYDROXYETHYL)ETHER / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsQuereda-Moraleda, I. / Grieco, A. / Botha, S. / Manna, A. / Ros, A. / Martin-Garcia, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)CNS2022-135713 Spain
Comunidad de MadridCAM_2019-T1BMD-15552 Spain
CitationJournal: Anal.Chem. / Year: 2024
Title: Cyclic Olefin Copolymer-Based Fixed-Target Sample Delivery Device for Protein X-ray Crystallography.
Authors: Manna, A. / Sonker, M. / Koh, D. / Steiger, M. / Ansari, A. / Hu, H. / Quereda-Moraleda, I. / Grieco, A. / Doppler, D. / de Sanctis, D. / Basu, S. / Orlans, J. / Rose, S.L. / Botha, S. / ...Authors: Manna, A. / Sonker, M. / Koh, D. / Steiger, M. / Ansari, A. / Hu, H. / Quereda-Moraleda, I. / Grieco, A. / Doppler, D. / de Sanctis, D. / Basu, S. / Orlans, J. / Rose, S.L. / Botha, S. / Martin-Garcia, J.M. / Ros, A.
History
DepositionMay 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)14,4964
Polymers14,3311
Non-polymers1653
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-15 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.300, 78.300, 38.100
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-356-

HOH

21A-371-

HOH

31A-395-

HOH

41A-399-

HOH

51A-404-

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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 6% (w/v) PEG 6000, 0.1 M sodium acetate pH 3.0, 20% (w/v) sodium chloride

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.6→39.15 Å / Num. obs: 16156 / % possible obs: 100 % / Redundancy: 4.51 % / CC star: 0.99 / R split: 0.158 / Net I/σ(I): 5
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 834 / CC star: 0.627 / R split: 1.563
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.809 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25057 834 5.2 %RANDOM
Rwork0.1908 ---
obs0.19378 15322 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.364 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.6→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 0 104 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121071
X-RAY DIFFRACTIONr_bond_other_d0.0010.016990
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.7791454
X-RAY DIFFRACTIONr_angle_other_deg0.5651.7962257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.801512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28410176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0172.365535
X-RAY DIFFRACTIONr_mcbond_other2.0082.364535
X-RAY DIFFRACTIONr_mcangle_it2.7584.238674
X-RAY DIFFRACTIONr_mcangle_other2.7794.245675
X-RAY DIFFRACTIONr_scbond_it3.6792.896536
X-RAY DIFFRACTIONr_scbond_other3.6772.904537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6635.072781
X-RAY DIFFRACTIONr_long_range_B_refined6.69324.71302
X-RAY DIFFRACTIONr_long_range_B_other6.6624.231287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 48 -
Rwork0.664 1112 -
obs--100 %

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