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- PDB-8p2q: Crystal structure of Hen Egg White Lysozyme co-crystallized with ... -

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Basic information

Entry
Database: PDB / ID: 8p2q
TitleCrystal structure of Hen Egg White Lysozyme co-crystallized with 10 mM TbXo4-OH
ComponentsLysozyme C
KeywordsHYDROLASE / HEWL / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0728
Polymers16,2581
Non-polymers8157
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-58 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.143, 77.143, 37.695
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-357-

HOH

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Components

#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
#2: Chemical ChemComp-WRT / TbXo4-OH


Mass: 614.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O5Tb
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / 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.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 1.72 Å3/Da / Density % sol: 28.69 %
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: Nov 22, 2019
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: 1.69→38.57 Å / Num. obs: 13258 / % possible obs: 99.9 % / Redundancy: 24.3 % / Biso Wilson estimate: 20.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Net I/σ(I): 34.3
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 23.8 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 15.8 / Num. unique obs: 1874 / CC1/2: 0.994 / Rpim(I) all: 0.054 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→38.57 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.9521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 661 5 %
Rwork0.1592 12550 -
obs0.161 13211 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.57 Å2
Refinement stepCycle: LAST / Resolution: 1.69→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 40 154 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441076
X-RAY DIFFRACTIONf_angle_d1.01191455
X-RAY DIFFRACTIONf_chiral_restr0.0812150
X-RAY DIFFRACTIONf_plane_restr0.005189
X-RAY DIFFRACTIONf_dihedral_angle_d13.2205393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.820.22811280.16422441X-RAY DIFFRACTION99.73
1.82-20.21271310.15392467X-RAY DIFFRACTION100
2.01-2.290.20531300.14672479X-RAY DIFFRACTION100
2.3-2.890.17351330.16692516X-RAY DIFFRACTION100
2.89-38.570.19381390.16012647X-RAY DIFFRACTION99.82
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)
10.103950971666-0.04909098027510.01190391748310.1177222480020.03742315103450.02047765293530.1079543970850.1731267140790.173893843229-0.086831177657-0.117054032152-0.205477383872-0.001863020256320.01904655957210.02264863918220.1583906866660.0062645000810.04469525818720.2148319945990.05502301056250.1821219672877.04253252368-15.6892240108-9.09499396336
20.0142672125223-0.010965257502-0.02802272326470.178982509450.1834896266440.207047714643-0.0443686288747-0.104062977947-0.1214930609160.05748337867860.114128559739-0.22722565403-0.05285683083150.2299521506490.01688012353870.1251763982180.00347884108781-0.03012987713850.200024252544-0.006269516515290.15417453372112.4236046989-23.08707763951.8589483744
30.0280752185507-0.03362444380880.007592937033020.0366092842806-0.009049974021310.0007851839526680.03841059519380.1040257935720.00403560728022-0.140584195018-0.03469255879830.1166407666490.00880769516102-0.04881908510221.52142793353E-50.1445651010020.03512192978850.007254419793230.163193104874-0.001303182475280.1698133422580.317028542723-21.1329475465-5.59726751989
40.0259388165398-0.0001115267456350.008336536605620.010236756929-0.01264995945460.03793828201420.2071948705250.0726326506811-0.05817135121330.105107180095-0.1694336150040.07766964606470.2590055299090.05031049356970.007291176277440.180997024047-0.005339094731660.03671835087430.1660319301010.0351825227690.226377144636-13.5625999866-18.67796432545.10928958497
50.06995720305430.04372782497790.07326224778930.04327135536390.06987136129890.112873398169-0.0795606407793-0.062961914546-0.03655966040630.03967534414280.03593603461760.0840309964598-0.009058340102960.10580238297-0.005806886516670.1572307881970.04628552109110.0107067438710.1516055006580.007010312923490.16242822871-6.07361215458-15.61791057357.32317429599
60.005851860172825.03254208128E-60.009512463725110.000114970950906-0.001837626414670.0298633325721-0.138294970029-0.1628897234570.1056048037530.3023894150470.164261530408-0.0395792445004-0.122984813555-0.0559239069523.92791125595E-50.2552203290010.0584330472127-0.002535766867710.267310823306-0.005336258338550.199549442322-4.0901599737-12.945522188714.3867444344
70.00899036997103-0.0103668082442-0.001809178771620.01877253621660.008998625150420.0062017581209-0.1770343011380.09117673489560.0391962891023-0.0260320117982-0.0319836776582-0.0529357550212-0.0261915179096-0.00910472563576-0.0001684168730240.1756028008130.00754173125372-0.01833165229290.1572363375130.01520738008730.194406886441-0.299553530393-8.670196090010.756018809658
80.01303464882950.00140319569418-0.002996453777910.0129514682616-0.01427213910150.0147257582132-0.00658197270657-0.03300995880040.2072949911450.1399526569840.182709854581-0.0613133434621-0.0236729493074-0.0207673372211-4.61026291606E-50.1717713925250.0108144858836-0.02616116404230.179041436314-0.01799026087690.2121508174035.86711417658-16.39594643525.96025782797
90.0309891346397-0.0762243332612-0.009391028109590.4898428608940.1415629079250.702751994722-0.190302349196-0.09589025730.01196068400980.2478225630740.01035867724690.2236905931380.0480326851961-0.276111305065-0.08649413441080.1578362421080.02260847167770.01512252196210.172752068647-0.003497210507010.1441561647890.182240483665-28.76104091794.14347846087
100.8259155529380.31912032194-0.06322486782660.279055872894-0.09705550578820.4471735228560.0126086121234-0.066771123597-0.120730592024-0.06370010634340.0190148206378-0.2181606515040.1709935264990.258430661360.3870292530310.1523638706670.0201994103610.03942263581770.188732853628-0.02994068318760.1612586273538.93575123671-28.2722027869-10.2204088815
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 42 )25 - 4225 - 42
44chain 'A' and (resid 43 through 50 )43 - 5043 - 50
55chain 'A' and (resid 51 through 68 )51 - 6851 - 68
66chain 'A' and (resid 69 through 78 )69 - 7869 - 78
77chain 'A' and (resid 79 through 88 )79 - 8879 - 88
88chain 'A' and (resid 89 through 99 )89 - 9989 - 99
99chain 'A' and (resid 100 through 114 )100 - 114100 - 114
1010chain 'A' and (resid 115 through 129 )115 - 129115 - 129

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