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- PDB-8owc: Crystal structure of Hen Egg White Lysozyme co-crystallized with ... -

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Basic information

Entry
Database: PDB / ID: 8owc
TitleCrystal structure of Hen Egg White Lysozyme co-crystallized with 10 mM TbXo4
ComponentsLysozyme C
KeywordsHYDROLASE / HEWL / Crystallophore / nucleating agent
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
Tb-Xo4 / TERBIUM(III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAlsalman, Z. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
Region Auvergne Rhone AlpesProject XO4_2.0 France
CitationJournal: Chemistry / Year: 2024
Title: Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network.
Authors: Roux, A. / Alsalman, Z. / Jiang, T. / Mulatier, J.C. / Pitrat, D. / Dumont, E. / Riobe, F. / Gillet, N. / Girard, E. / Maury, O.
History
DepositionApr 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)17,24411
Polymers16,2581
Non-polymers98610
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-89 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.474, 77.474, 37.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-207-

CL

21A-334-

HOH

31A-419-

HOH

41A-435-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O4Tb / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.73 Å3/Da / Density % sol: 28.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 650 mM sodium chloride, 100mM sodium acetate pH=4.6. Drops were set by mixing one volume of protein solution at 20mg/ml with one volume of 10mM TbXo4 and with one volume of the well solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.648 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2020
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.648 Å / Relative weight: 1
ReflectionResolution: 1.7→37.49 Å / Num. obs: 13059 / % possible obs: 99.7 % / Redundancy: 24 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.026 / Net I/σ(I): 22.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 23.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 9 / Num. unique obs: 1848 / CC1/2: 0.986 / Rpim(I) all: 0.073 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.75 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.4769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 651 5 %
Rwork0.1753 12364 -
obs0.1771 13015 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 38 137 1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551072
X-RAY DIFFRACTIONf_angle_d0.69391450
X-RAY DIFFRACTIONf_chiral_restr0.0429150
X-RAY DIFFRACTIONf_plane_restr0.0038189
X-RAY DIFFRACTIONf_dihedral_angle_d12.7549377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.2961260.20522404X-RAY DIFFRACTION99.37
1.83-2.020.24081290.19342424X-RAY DIFFRACTION99.84
2.02-2.310.22281280.17762448X-RAY DIFFRACTION100
2.31-2.910.20191310.18482491X-RAY DIFFRACTION100
2.91-33.750.1961370.16462597X-RAY DIFFRACTION99.42
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)
10.410291862565-0.501772536563-0.1850119648630.6594259709180.1088770660590.4446750060330.1579385446310.359409094181-0.203834409475-0.110550309286-0.1615277086020.2282051816840.249639441829-0.126255217849-0.05407251525050.1884529649130.00525412003916-0.09908446755890.411061732987-0.150807883910.195549508738-7.3415267536816.12800385099.74562893125
20.127628231593-0.0251353972146-0.1154178213690.05172598382470.03745997207250.114545598261-0.199444985169-0.108436068948-0.1622768069850.1327742058640.007365742509250.0325366343268-0.0037920659497-0.246804641198-2.51855646232E-50.2369358995460.0564409676558-0.001664678559740.239079435706-0.0002810681964050.2240781548315.7430597165615.132724114628.2701828265
30.003706416347990.00998486355549-0.007796982978760.0202498806932-0.01822692057930.0132395032308-0.268382341312-0.0160421455242-0.127272274811-0.0451574065711-0.1033197585030.0968764523280.0152967669109-0.08420176734429.13399056307E-50.2343509646850.004763058141980.01314858314960.237629382301-0.04587142198850.3215889644040.5345071222628.8382992369619.3326606264
40.009884433276730.001300704957480.0009959228312230.00984650920991-0.01711280587770.0341687628499-0.004721741151150.103472333971-0.3572050949740.2361138077420.04864013520570.07096007086580.0484866874598-0.0531264392839-0.0001093870900170.2544595193780.009881549032880.01742357735520.262370805414-0.0401048754130.301239725091-5.7507071500417.109939341525.1096107325
50.003602489407290.00401454868771-0.007578026365510.03584054993370.008843106331660.0239694345314-0.152094434817-0.02032754638720.08295629170390.0228464179180.0300042495192-0.205182779271-0.03657551396060.394789238027.59797517171E-50.1942730862110.0151548166658-0.01839389196450.23335251882-0.0291391924210.2182144715430.58382087627929.272949782122.2661509
60.0867274459849-0.01666574004530.2090839372040.411360615308-0.4494084990840.9159224601380.1889784335250.2977564542120.2580361402740.00388295466082-0.003404487619060.283351321721-0.104493545271-0.1315870269910.3304516436440.224378520840.0699241539509-0.0719361954320.387507046236-0.001166913621260.283239244906-8.8534093102428.23620368248.39930663088
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 14 )1 - 141 - 14
22chain 'A' and (resid 51 through 78 )51 - 7851 - 78
33chain 'A' and (resid 79 through 88 )79 - 8879 - 88
44chain 'A' and (resid 89 through 100 )89 - 10089 - 100
55chain 'A' and (resid 101 through 114 )101 - 114101 - 114
66chain 'A' and (resid 115 through 129 )115 - 129115 - 129

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