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- PDB-6sik: SAD structure of Hen Egg White Lysozyme recovered by continuous r... -

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Basic information

Entry
Database: PDB / ID: 6sik
TitleSAD structure of Hen Egg White Lysozyme recovered by continuous rotation data collection and univariate analysis
ComponentsLysozyme C
KeywordsHYDROLASE / Univariate analysis / Single-wavelength X-ray Anomalous Diffraction / Continuous rotation / Hen Egg White Lysozyme
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
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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61007015159 Å
AuthorsGarcia-Bonete, M.J. / Katona, G.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Acta Crystallogr.,Sect.A / Year: 2019
Title: Bayesian machine learning improves single-wavelength anomalous diffraction phasing.
Authors: Garcia-Bonete, M.J. / Katona, G.
History
DepositionAug 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)16,86915
Polymers16,2581
Non-polymers61114
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Commercially obtained from Sigma-Aldrich (St Louis, MO)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-80 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.870, 78.870, 36.880
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-332-

HOH

21A-401-

HOH

31A-472-

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, 193 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 29.1 % / Description: Tetragonal lysozyme crystals, size 200 um
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 50mM Na acetate pH 4.5 1M NaCl 25% Ethylene glycol / Temp details: Temperature controlled room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.61→39.435 Å / Num. obs: 28771 / % possible obs: 99.9 % / Redundancy: 39.2 % / Biso Wilson estimate: 11.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 47.53
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 8.84 / Num. unique obs: 2102 / CC1/2: 0.985 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.61007015159→39.435 Å / SU ML: 0.106922402014 / Cross valid method: FREE R-VALUE / σ(F): 1.33383088077 / Phase error: 15.8991856531
RfactorNum. reflection% reflection
Rfree0.162699648796 1445 5.02416466743 %
Rwork0.139268579627 --
obs0.140491952434 28761 99.9096814534 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.0631512486 Å2
Refinement stepCycle: LAST / Resolution: 1.61007015159→39.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 29 179 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005127201102351088
X-RAY DIFFRACTIONf_angle_d0.80438212391468
X-RAY DIFFRACTIONf_chiral_restr0.0537365634339149
X-RAY DIFFRACTIONf_plane_restr0.00433492600398194
X-RAY DIFFRACTIONf_dihedral_angle_d9.53294540413649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6101-1.66760.1882497010491430.1652256447052718X-RAY DIFFRACTION99.2024965326
1.6676-1.73440.1919712510331450.1464868142722712X-RAY DIFFRACTION99.9300454704
1.7344-1.81330.2023489112451430.1501784769242736X-RAY DIFFRACTION100
1.8133-1.90890.1702742867311460.1345821920812731X-RAY DIFFRACTION100
1.9089-2.02850.172476503691440.1298894787172749X-RAY DIFFRACTION100
2.0285-2.18510.1566417213441410.1337660236142728X-RAY DIFFRACTION100
2.1851-2.4050.1455886259981440.1301207696062734X-RAY DIFFRACTION100
2.405-2.75290.1713908745061460.1487493801572721X-RAY DIFFRACTION100
2.7529-3.46810.1383868190771490.1383172771582751X-RAY DIFFRACTION100
3.4681-39.40.1618566808871440.1372317929062736X-RAY DIFFRACTION99.9652898299
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)
10.3859242374760.262300768397-0.2885562118190.736607192525-0.04203351087011.04301096972-0.0592691530427-0.0243771772531-0.168200395811-0.1336814282110.0167473247257-0.07245869665360.1279749519960.05426440884560.006109706202740.1190222845350.01318403666250.01459668208480.0903181410356-0.03037329119950.12252950299522.657529392433.90782609741.11551307556
21.384829167620.2308463355150.6592780862040.440316498914-0.3336698988250.8116322850560.135121705927-0.0208274250241-0.363474880843-0.114401921742-0.0614020695475-0.03045231238910.2257452620870.00161294797431-0.1609573492960.120066970592-0.00300460228130.002644747974320.06193193939550.0121503960410.12805673449115.699542799629.457984268910.7427354191
30.1633057743530.116439072344-0.06225959296160.2744716658920.05123379655660.145639581332-0.0388582468009-0.0496457891735-0.00129923660124-0.09094418312230.0237715107075-0.0123458209812-0.0227576207749-0.006961782635510.01275589622920.0690019860069-0.009517624861970.002929608562430.0696833582471-0.009688413434340.085278627769817.823124519140.0022419213.92663710914
41.354898024390.3998717476460.4033347214060.4538535310370.05652674652290.550369962060.0686694979147-0.3956160487710.349564206852-0.00954821701125-0.05866487938780.143029141727-0.158219458448-0.2861175916290.05914564105760.1453253884430.01876493522540.03402715185050.165717974704-0.04792522069410.12304554249320.127616904452.5679244713.2733339302
53.471903355533.17669036531.770612948455.533316108751.070060285122.778536877650.0551557656447-0.120144541925-0.0954777636451-0.00741960406759-0.0084849225815-0.004378232235120.153582717367-0.128697164076-0.05414732750310.0756535111599-0.003996315814680.0004299792345550.0684410760999-0.002516054886310.055240817078421.75165489645.078832758610.929535581
60.7755532924210.392026346813-0.1013705415451.24047171584-0.3794798953590.1239444381810.157184270561-0.1505004297550.1027923365560.424279220718-0.167384139223-0.0482143617805-0.0487783619135-0.1202276131450.08735585354040.123541726441-0.02728672322550.008522012461960.132548026328-0.01138396533830.077359862989722.832263343147.366917089818.9685046419
70.6534063829350.5031788859290.09716058973360.772344572495-0.3602516247340.4362155063620.108802030649-0.140473181034-0.1745920848570.152262309875-0.119950137987-0.1982871788320.004579206531550.0584695237069-0.01005581529040.0859540294555-0.013347324326-0.00403173815580.08761653676740.009317097961620.094526417803124.541762124339.645571018315.3723643606
80.5582541472780.256880812660.394469215110.4356859540560.1118967753120.3729413601840.0225962210586-0.179211139880.03195464669750.112410422444-0.07162286557160.117532229964-0.146089301248-0.1143257464490.05533459425510.0966846291377-0.00192667936065-0.005734347227960.07020196629210.001913772133930.081662781439211.752291233340.404141251413.6047502266
90.969326503259-0.385379639736-0.2915403809170.305899576379-0.167736079930.6748557827250.1039958323090.261234640038-0.459135657131-0.0354895006114-0.116652569137-0.02162436300190.372856538612-0.113572579545-0.06903479374270.1330500722530.00751366532294-0.0229739522340.101584149333-0.04166574438480.16836884154112.285331824331.70639262040.665035497243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 86 )
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 147 )

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