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Entry
Database: PDB / ID: 5njp
TitleMix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 1s time-delay, phased with 1HEW
ComponentsLysozyme C
KeywordsHYDROLASE / competitive inhibitor glycoside hydrolase
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
triacetyl-beta-chitotriose / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOberthuer, D. / Meents, A. / Beyerlein, K.R. / Chapman, H.N. / Lieseke, J.
CitationJournal: IUCrJ / Year: 2017
Title: Mix-and-diffuse serial synchrotron crystallography.
Authors: Beyerlein, K.R. / Dierksmeyer, D. / Mariani, V. / Kuhn, M. / Sarrou, I. / Ottaviano, A. / Awel, S. / Knoska, J. / Fuglerud, S. / Jonsson, O. / Stern, S. / Wiedorn, M.O. / Yefanov, O. / ...Authors: Beyerlein, K.R. / Dierksmeyer, D. / Mariani, V. / Kuhn, M. / Sarrou, I. / Ottaviano, A. / Awel, S. / Knoska, J. / Fuglerud, S. / Jonsson, O. / Stern, S. / Wiedorn, M.O. / Yefanov, O. / Adriano, L. / Bean, R. / Burkhardt, A. / Fischer, P. / Heymann, M. / Horke, D.A. / Jungnickel, K.E.J. / Kovaleva, E. / Lorbeer, O. / Metz, M. / Meyer, J. / Morgan, A. / Pande, K. / Panneerselvam, S. / Seuring, C. / Tolstikova, A. / Lieske, J. / Aplin, S. / Roessle, M. / White, T.A. / Chapman, H.N. / Meents, A. / Oberthuer, D.
History
DepositionMar 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,0535
Polymers14,3311
Non-polymers7214
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-14 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.610, 79.610, 38.300
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-344-

HOH

21A-349-

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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 274 K / Method: batch mode / pH: 3.5
Details: Crystals with sizes between 6 and 8 um in diameter were obtained by adding three parts of precipitant (1M NaCl, 40% ethylene glycol (v/v), 15% PEG4000 (w/v), 50 mM acetate buffer at pH 3.5, ...Details: Crystals with sizes between 6 and 8 um in diameter were obtained by adding three parts of precipitant (1M NaCl, 40% ethylene glycol (v/v), 15% PEG4000 (w/v), 50 mM acetate buffer at pH 3.5, filtered through 450 nm filter) to one part of lysozyme (Sigma-Aldrich, 126 mg/ml dissolved in50 mM acetate buffer, pH 3.5, filtered through 100 nm filter) at 274K (ThermoStat C, Eppendorf, Germany). The resulting mixture was immediately subjected to rapid mixing and incubated for 30 minutes at 274K.

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→21.81 Å / Num. obs: 14038 / % possible obs: 100 % / Redundancy: 3743 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 0.99 / R split: 0.0406 / Net I/σ(I): 14.53
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 165 % / Mean I/σ(I) obs: 0.56 / Num. unique obs: 1339 / CC1/2: 0.14 / R split: 2.159 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HEW

1hew


Resolution: 1.7→21.813 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1401 10 %Random selectiom
Rwork0.1702 ---
obs0.1732 14015 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 46 60 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041079
X-RAY DIFFRACTIONf_angle_d0.6371468
X-RAY DIFFRACTIONf_dihedral_angle_d9.629635
X-RAY DIFFRACTIONf_chiral_restr0.04160
X-RAY DIFFRACTIONf_plane_restr0.004187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.76080.38381340.38941205X-RAY DIFFRACTION99
1.7608-1.83130.3451360.31171238X-RAY DIFFRACTION100
1.8313-1.91460.30081390.25181249X-RAY DIFFRACTION100
1.9146-2.01540.2411380.21381238X-RAY DIFFRACTION100
2.0154-2.14160.27121370.20411238X-RAY DIFFRACTION100
2.1416-2.30680.20941400.17641255X-RAY DIFFRACTION100
2.3068-2.53860.20071400.17041258X-RAY DIFFRACTION100
2.5386-2.90520.19781410.18461264X-RAY DIFFRACTION100
2.9052-3.65750.1991430.15541294X-RAY DIFFRACTION100
3.6575-21.81440.15881530.13611375X-RAY DIFFRACTION100

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