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- PDB-6a10: Crystal structure of hen egg white lysozyme crystallized by ammon... -

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Basic information

Entry
Database: PDB / ID: 6a10
TitleCrystal structure of hen egg white lysozyme crystallized by ammonium sulfate
ComponentsLysozyme C
KeywordsHYDROLASE
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsKitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K08458 Japan
CitationJournal: Cryst.Growth Des. / Year: 2019
Title: Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization
Authors: Kitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _struct_site_gen.auth_seq_id
Revision 2.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
C: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,95413
Polymers42,9933
Non-polymers96110
Water13,781765
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7155
Polymers14,3311
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6194
Polymers14,3311
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6194
Polymers14,3311
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.399, 57.971, 57.618
Angle α, β, γ (deg.)115.970, 105.200, 98.810
Int Tables number1
Space group name H-MP1

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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.: 3 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.65 Å3/Da / Density % sol: 53.65 % / Mosaicity: 0.597 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.2M ammonium sulfate, 6%(v/v) 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 151134 / % possible obs: 91.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.06 / Χ2: 1.026 / Net I/σ(I): 12.8 / Num. measured all: 293247
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.13-1.151.90.35973880.7740.3590.5080.99789.1
1.15-1.171.90.30473590.8220.3040.431.03990
1.17-1.1920.24874620.8730.2480.351.06190.2
1.19-1.221.90.21974880.890.2190.3091.0690.1
1.22-1.2420.1975140.9140.190.2681.07291.4
1.24-1.2720.16175800.9380.1610.2281.06191.5
1.27-1.320.13975830.9490.1390.1971.05191.6
1.3-1.3420.12376110.9560.1230.1741.05192
1.34-1.3820.10776520.9640.1070.1521.04292.5
1.38-1.4220.0976900.9750.090.1271.01193.1
1.42-1.4720.07877090.9790.0780.1111.01393.4
1.47-1.5320.06877980.9830.0680.0960.9993.9
1.53-1.620.06177890.9840.0610.0860.98594.5
1.6-1.691.90.05778450.9850.0570.080.9995
1.69-1.791.90.05478490.9860.0540.0760.99695
1.79-1.931.90.04978730.9870.0490.0690.99495.6
1.93-2.131.90.04478870.9890.0440.0631.02595.2
2.13-2.431.80.03677640.9920.0360.0511.00593.9
2.43-3.071.90.02775610.9950.0270.0381.0391.5
3.07-501.90.02257320.9950.0220.0321.05569.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WLD

4wld


Resolution: 1.13→19.295 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 16.99
RfactorNum. reflection% reflection
Rfree0.1761 7626 5.05 %
Rwork0.1633 --
obs0.164 151130 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.65 Å2 / Biso mean: 17.77 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 1.13→19.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 50 765 3818
Biso mean--25.79 32.03 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113115
X-RAY DIFFRACTIONf_angle_d1.3654203
X-RAY DIFFRACTIONf_chiral_restr0.093432
X-RAY DIFFRACTIONf_plane_restr0.007543
X-RAY DIFFRACTIONf_dihedral_angle_d11.7481095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1304-1.14320.26952130.2764515472886
1.1432-1.15670.2622240.25464779500390
1.1567-1.17080.23542540.24094601485590
1.1708-1.18560.23352650.22454756502190
1.1856-1.20120.2282690.22174770503991
1.2012-1.21760.23452620.21794648491090
1.2176-1.2350.22782340.20574808504292
1.235-1.25350.22482390.2014830506991
1.2535-1.2730.20842520.19114761501392
1.273-1.29390.19162680.18664760502891
1.2939-1.31620.1912810.17794818509993
1.3162-1.34010.19822700.17754789505992
1.3401-1.36590.19192300.17254893512393
1.3659-1.39380.19962500.16424884513493
1.3938-1.42410.17842580.15844843510193
1.4241-1.45720.19022580.15534884514294
1.4572-1.49360.17752850.15484886517194
1.4936-1.5340.17122450.14714978522394
1.534-1.57910.1632610.1474892515395
1.5791-1.63010.15422880.13824959524795
1.6301-1.68830.15272860.13984949523595
1.6883-1.75580.14212410.14544983522495
1.7558-1.83570.16982730.14744939521295
1.8357-1.93240.15432670.14575034530196
1.9324-2.05330.16432760.14255017529395
2.0533-2.21170.15992810.14034904518594
2.2117-2.43380.16032510.13974940519194
2.4338-2.78510.15552410.15454862510393
2.7851-3.50550.16892320.16724376460884
3.5055-19.29820.21471720.20893446361865

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