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

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Basic information

Entry
Database: PDB / ID: 8pob
TitleCrystal structure of Hen Egg White Lysozyme co-crystallized with 10 mM TbXo4-SO3
ComponentsLysozyme C
KeywordsHYDROLASE / EWL / Crystallophore variants / 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
TERBIUM(III) ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsAlsalman, Z. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
Other governmentProject XO4_2.0 France
Citation
Journal: 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.
#1: Journal: Chem Sci / Year: 2017
Title: Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
Authors: Engilberge, S. / Riobe, F. / Di Pietro, S. / Lassalle, L. / Coquelle, N. / Arnaud, C.A. / Pitrat, D. / Mulatier, J.C. / Madern, D. / Breyton, C. / Maury, O. / Girard, E.
History
DepositionJul 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 23, 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)17,33311
Polymers16,2581
Non-polymers1,07510
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-76 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.404, 77.404, 37.602
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-208-

CL

21A-335-

HOH

31A-393-

HOH

41A-415-

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, 127 molecules

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


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-ZW0 / 6-[[4-[(6-carboxypyridin-2-yl)methyl]-7-(3-sulfopropyl)-1,4,7-triazonan-1-yl]methyl]pyridine-2-carboxylic acid


Mass: 521.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N5O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / 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.: 117 / 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: 28.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 950 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: 1.74→38.7 Å / Num. obs: 12161 / % possible obs: 99.9 % / Redundancy: 24.1 % / Biso Wilson estimate: 33.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.028 / Net I/σ(I): 0.248
Reflection shellResolution: 1.74→1.84 Å / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 0.04 / Num. unique obs: 1719 / CC1/2: 0.929 / Rpim(I) all: 0.184

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→38.7 Å / SU ML: 0.2858 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.3627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 607 5.01 %
Rwork0.1803 11513 -
obs0.1827 12120 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.9 Å2
Refinement stepCycle: LAST / Resolution: 1.74→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 45 117 1163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01451068
X-RAY DIFFRACTIONf_angle_d1.29121446
X-RAY DIFFRACTIONf_chiral_restr0.0746149
X-RAY DIFFRACTIONf_plane_restr0.01187
X-RAY DIFFRACTIONf_dihedral_angle_d13.5526391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.920.36471480.30562799X-RAY DIFFRACTION99.56
1.92-2.20.22771490.18742841X-RAY DIFFRACTION100
2.2-2.770.25621510.18462863X-RAY DIFFRACTION100
2.77-38.70.20561590.16613010X-RAY DIFFRACTION99.78
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)
10.228130923948-0.03477228157780.0523128797980.2815877698410.0614629913610.03023113584380.2261123755890.5283789344780.361010494296-0.302043660434-0.295794961663-0.150951399397-0.3201260712370.230846480539-0.02425131256240.251380851054-0.02202975968960.05782310284670.3887004301180.1188178743840.310744622847.59655863567-16.0187281869-8.85904424429
20.0291378408372-0.0362663525638-0.0644219788940.3687880880250.006952080695280.160334943358-0.181729599669-0.227548387163-0.08773203063450.03887225647630.0774205023995-0.8598641765720.1038953391070.517254187821-0.004257324389180.3160973861550.00510172896566-0.05263266811870.4739813296020.0313099160540.42696042514111.9330962195-23.06187688782.23196360194
30.911378645139-0.110927916003-0.174900979170.4479449799880.1410319343090.183433694249-0.0572107521550.004900209443130.1032083591380.1370581310980.0154447927919-0.03589177057940.01131720081110.0652301640037-2.10548646563E-50.2665948427610.04069695273960.006656025597790.2932746283270.03020702210270.289166371958-4.37197459867-16.43858391673.52129239919
40.0642252880063-0.00717121574549-0.002174831213770.0192212182315-0.01900944251530.0697895613912-0.0778742328762-0.063386236050.1524440949680.3566715324660.091606209232-0.150914780885-0.1291336763250.09636621321593.89526874632E-50.2899910824480.0126218751884-0.0270203895150.325480633640.02463110618750.3653485778035.61578592493-16.49294240125.89958107561
50.08267731289270.09625639875460.003455904205140.223214906677-0.1381231334340.158637144786-0.182368004409-0.262761462804-0.03002230328850.3241622186730.1369678128030.2587124876330.00457833415635-0.3407938938092.91160920496E-50.2797984526310.02060218475780.02995400167670.3388715545280.03981601568820.3070642167170.0558028985786-28.87950803174.16514221815
60.6373947705860.329116531975-1.086289764020.518691571622-0.4428896265432.20886474072-0.03933147348560.2600773769610.0257551867955-0.1497985259910.208765823349-0.2200156168710.5695672014890.1983879558350.1930831161670.2756249814090.0335366966310.06365091945750.426815730388-0.006064012650520.3310939584228.73210640091-28.3879793755-10.2698521258
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 15 through 24 )15 - 2415 - 24
33chain 'A' and (resid 25 through 88 )25 - 8825 - 88
44chain 'A' and (resid 89 through 99 )89 - 9989 - 99
55chain 'A' and (resid 100 through 114 )100 - 114100 - 114
66chain 'A' and (resid 115 through 129 )115 - 129115 - 129

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