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Entry
Database: PDB / ID: 5njs
TitleMix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 50s time-delay, phased with 1HEW
ComponentsLysozyme C
KeywordsHYDROLASE / competitive inhibitor glycoside hydrolase
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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

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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)15,0886
Polymers14,3311
Non-polymers7575
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-21 kcal/mol
Surface area6570 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-302-

HOH

21A-348-

HOH

31A-360-

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 / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.12 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 4, 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→22.681 Å / Num. obs: 14040 / % possible obs: 100 % / Redundancy: 4932 % / CC1/2: 0.99 / R split: 0.0349 / Net I/σ(I): 16.65
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 267 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 1352 / CC1/2: 0.39 / R split: 1.1245 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HEW

1hew


Resolution: 1.7→22.681 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 1403 10.01 %same as 5NJR
Rwork0.1641 ---
obs0.1675 14016 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→22.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 47 60 1108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041070
X-RAY DIFFRACTIONf_angle_d0.6231454
X-RAY DIFFRACTIONf_dihedral_angle_d9.35629
X-RAY DIFFRACTIONf_chiral_restr0.042159
X-RAY DIFFRACTIONf_plane_restr0.003184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.76080.3491360.32291216X-RAY DIFFRACTION100
1.7608-1.83130.30761370.26151238X-RAY DIFFRACTION100
1.8313-1.91460.22121390.1991250X-RAY DIFFRACTION100
1.9146-2.01540.2381380.18471236X-RAY DIFFRACTION100
2.0154-2.14160.24151370.18261237X-RAY DIFFRACTION100
2.1416-2.30680.22151400.16231251X-RAY DIFFRACTION100
2.3068-2.53870.18871400.16361258X-RAY DIFFRACTION100
2.5387-2.90540.21881400.17791260X-RAY DIFFRACTION100
2.9054-3.6580.17671430.1561293X-RAY DIFFRACTION100
3.658-22.68250.171530.13751374X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7627-0.6346-0.16872.40050.07023.0860.10520.1436-0.3064-0.37970.00030.36020.5211-0.1857-0.05540.37-0.0188-0.09510.3515-0.060.3715-6.633516.59729.5773
23.91421.35390.62472.009-0.37461.7331-0.02760.248-0.11740.26430.00780.8290.2123-0.51010.0630.2489-0.00440.02730.379-0.05750.3593-11.736524.028820.6152
32.0625-1.65190.52283.1041-0.1670.93510.20020.12620.033-0.3316-0.1596-0.18850.00520.0215-0.05420.26460.0279-0.01770.2857-0.00580.28870.524722.045313.0016
46.1634.3414.81525.40375.09995.19650.11760.34920.1179-0.48610.572-0.6166-0.69730.6044-0.75360.39-0.0244-0.03420.359-0.04310.329714.718120.213924.1814
52.8156-1.9315-0.71463.2392-0.76952.1136-0.1518-0.32970.10690.26380.1285-0.0893-0.03910.2405-0.04020.27520.0348-0.01770.3029-0.02270.26017.281317.075526.1191
61.9977-1.24070.97273.50040.18334.031-0.594-1.75480.00350.75820.463-0.2191-0.3371-0.24540.21260.46840.12480.00590.55530.01330.36755.102414.641933.4503
74.6326-0.65262.19051.70360.1813.0169-0.1270.207-0.5962-0.2730.19630.50390.13030.0691-0.13120.3910.0239-0.01360.2939-0.03310.43091.59249.826819.9007
82.8875-0.565-0.2678.2964.0624.0462-0.2507-0.0846-0.41130.5757-0.06240.76120.4333-0.28330.26110.2979-0.02090.06750.3019-0.02150.3483-5.071717.381124.7269
93.8881-0.2556-2.31712.9709-0.43176.3301-0.0787-0.35810.31340.24530.1459-0.2413-0.20990.68350.00640.22950.0096-0.01680.2908-0.04560.29020.087229.836922.5923
105.06233.15383.27585.15263.12815.4082-0.31450.29570.426-0.5975-0.09860.7583-0.1344-0.62230.33050.39470.0092-0.06190.44750.02040.3963-8.231228.54538.0486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 88 )
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 99 )
9X-RAY DIFFRACTION9chain 'A' and (resid 100 through 114 )
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 129 )

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