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- PDB-8rpm: Lysozyme structure based on automated real-time serial crystallog... -

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Basic information

Entry
Database: PDB / ID: 8rpm
TitleLysozyme structure based on automated real-time serial crystallography data processing using CrystFEL
ComponentsLysozyme C
KeywordsHYDROLASE / JINXED / real-time data processing
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 (bird)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhite, T.A. / Oberthuer, D. / Henkel, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission85764European Union
CitationJournal: Iucrj / Year: 2025
Title: Real-time data processing for serial crystallography experiments.
Authors: White, T. / Schoof, T. / Yakubov, S. / Tolstikova, A. / Middendorf, P. / Karnevskiy, M. / Mariani, V. / Henkel, A. / Klopprogge, B. / Hannappel, J. / Oberthuer, D. / De Gennaro Aquino, I. / ...Authors: White, T. / Schoof, T. / Yakubov, S. / Tolstikova, A. / Middendorf, P. / Karnevskiy, M. / Mariani, V. / Henkel, A. / Klopprogge, B. / Hannappel, J. / Oberthuer, D. / De Gennaro Aquino, I. / Egorov, D. / Munke, A. / Sprenger, J. / Pompidor, G. / Taberman, H. / Gruzinov, A. / Meyer, J. / Hakanpaa, J. / Gasthuber, M.
History
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 22, 2025Group: 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

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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)14,4254
Polymers14,3311
Non-polymers943
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-29 kcal/mol
Surface area6530 Å2
Unit cell
Length a, b, c (Å)79.200, 79.200, 38.000
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-343-

HOH

21A-352-

HOH

31A-370-

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 (bird) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 40.84 %
Crystal growTemperature: 295 K / Method: microfluidic / pH: 3.5
Details: Just in-time crystallization (JINXED): a lysozyme solution in acetate buffer (pH 3.5) was mixed with crystallization solution on a running conveyor belt using 3D printed micro nozzles. ...Details: Just in-time crystallization (JINXED): a lysozyme solution in acetate buffer (pH 3.5) was mixed with crystallization solution on a running conveyor belt using 3D printed micro nozzles. Crystallization solution: N,N',N'',N''',N'''',N'''''-Hexaacetyl chitohexaose in 33 mM acetate buffer, pH3.5, 6.67% (w/v) PEG4000, 2.07 M NaCl, 6.67% DMSO

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→79.365 Å / Num. obs: 11716 / % possible obs: 100 % / Redundancy: 373.9 % / CC1/2: 0.98 / CC star: 0.995 / R split: 0.117 / Net I/σ(I): 5.292
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 248.5 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 1118 / CC1/2: 0.446 / CC star: 0.785 / R split: 1.115 / % possible all: 100
Serial crystallography sample deliveryDescription: JINXED on TapeDrive / Method: injection
Serial crystallography data reductionFrame hits: 60200 / Frames total: 200000 / Lattices indexed: 14322

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.21rc1-4903refinement
PDB-REDOrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.231 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22215 637 5.8 %RANDOM
Rwork0.18466 ---
obs0.18695 10264 93.31 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 71 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121021
X-RAY DIFFRACTIONr_bond_other_d0.0010.016938
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.7771381
X-RAY DIFFRACTIONr_angle_other_deg0.4911.7922136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.72511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4410166
X-RAY DIFFRACTIONr_chiral_restr0.0720.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_mcbond_it3.7793.022515
X-RAY DIFFRACTIONr_mcbond_other3.7563.02515
X-RAY DIFFRACTIONr_mcangle_it4.5945.41642
X-RAY DIFFRACTIONr_mcangle_other4.645.417643
X-RAY DIFFRACTIONr_scbond_it5.8823.66506
X-RAY DIFFRACTIONr_scbond_other5.8743.657506
X-RAY DIFFRACTIONr_scangle_other8.4566.417740
X-RAY DIFFRACTIONr_long_range_B_refined9.59930.241234
X-RAY DIFFRACTIONr_long_range_B_other9.60230.031222
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 38 -
Rwork0.381 586 -
obs--75.91 %

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