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

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Basic information

Entry
Database: PDB / ID: 6sij
TitleSAD structure of Hen Egg White Lysozyme recovered by continuous rotation data collection and multivariate analysis of Friedel pairs
ComponentsLysozyme C
KeywordsHYDROLASE / Multivariate 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: 1.6101802385 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

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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
Water3,135174
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 area2110 Å2
ΔGint-80 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.070, 79.070, 36.980
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-351-

HOH

21A-400-

HOH

31A-469-

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, 188 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.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.75 Å3/Da / Density % sol: 29.7 % / 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→39.535 Å / Num. obs: 28771 / % possible obs: 99.9 % / Redundancy: 39.2 % / Biso Wilson estimate: 11.7 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: 1.6101802385→39.535 Å / SU ML: 0.120331246052 / Cross valid method: FREE R-VALUE / σ(F): 0.0499243409143 / Phase error: 15.2035774088
RfactorNum. reflection% reflection
Rfree0.167330244174 1402 4.90398404981 %
Rwork0.140585517396 --
obs0.141874113995 28589 98.5759602786 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.0291672277 Å2
Refinement stepCycle: LAST / Resolution: 1.6101802385→39.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 29 174 1204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005807379455251088
X-RAY DIFFRACTIONf_angle_d0.8194048803311468
X-RAY DIFFRACTIONf_chiral_restr0.0552173424913149
X-RAY DIFFRACTIONf_plane_restr0.00452953116727194
X-RAY DIFFRACTIONf_dihedral_angle_d9.22846516367649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6102-1.66770.1936082854271540.1595336623262680X-RAY DIFFRACTION98.0962270682
1.6677-1.73450.2056300083731620.1427141546512671X-RAY DIFFRACTION98.3339118362
1.7345-1.81340.1902420109241280.1546587692362748X-RAY DIFFRACTION98.3584131327
1.8134-1.90910.1980052620131350.1408297351992694X-RAY DIFFRACTION98.6057859881
1.9091-2.02870.1684992702021320.1316685518612760X-RAY DIFFRACTION98.5013623978
2.0287-2.18530.1570067193981430.1327685136742723X-RAY DIFFRACTION99.0667127549
2.1853-2.40520.1400094526031270.1277827978912734X-RAY DIFFRACTION98.8255613126
2.4052-2.75310.1595215360221370.1474300829152720X-RAY DIFFRACTION98.5852311939
2.7531-3.46830.1651706223271400.1406738049932720X-RAY DIFFRACTION98.5187736824
3.4683-39.50.1615029839791440.1421092636652737X-RAY DIFFRACTION99.0034364261
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)
11.89045732294-1.85867274752-1.097305332434.112464570080.05399139450664.00473687988-0.0743853814113-0.0377408197246-0.2275592422840.1687101814220.02355369851520.1509774717740.126099673528-0.1217892686750.03702436232570.098323244809-0.01842972046550.02515528994930.07758587763750.03648356368620.1276984281955.661828354233.327478657627.7464930055
26.179884463530.182009288660.005220913617572.82666495234-0.2055172292751.412144702480.1690387449480.14755573045-0.4772367930320.145708463459-0.1406074163370.07188869930740.174722619447-0.09455113726330.01320078256810.1193235105150.00806133941078-0.001372307715710.0518790866916-0.02261321194690.13700970115363.022006483928.011003069116.4693537998
30.807050828392-0.641333329790.04890000274891.375840069-0.2302739293190.954141972064-0.01805793099070.1301114230890.08976029476130.07783662365280.0288676925653-0.0989987372778-0.1070527337740.03731044017060.03336017913620.0500506351656-0.00451360201780.01058454445750.05287851895460.02548656607230.067849376264560.577967750745.037528552920.6488902852
41.55809071633-0.800581220749-0.05493094453572.52531108381.599926904621.475451772450.1374142754090.2657688091920.0730064321832-0.322505470444-0.161289073733-0.01508469585-0.0125593134250.136769681879-0.007204928357810.07588886934610.01414436966320.009213530628830.08160986654910.01982761900070.060624833020855.932992159947.226291065711.2664538465
51.43902011615-1.057889387760.3986251983281.112841266750.0368660860960.6871249857590.1079095305840.156534106913-0.0898892321192-0.0964662882331-0.1033209033920.0800494112818-0.0486488141045-0.031672325790.005645479855380.07385519647830.00371192807357-0.006053545905540.0517781605432-0.004288308502380.068655404707458.795546018839.836908785112.6770953878
64.817941171681.18548449582-1.666268054590.757529225457-0.8645493936885.149769883880.0255079572615-0.305495524059-0.335032790225-0.0416218519684-0.1306091226-0.1496931029750.5045583564940.3767470429130.07551021586410.08999065957050.0232679768644-0.009566195870890.08047264803130.02291124314080.10032653909471.90211169634.242544890626.1393353061
75.845872794045.02157521083-5.086829441898.82365419978-3.177622412368.8768597785-0.115278784867-0.252696201555-0.5145140361740.1086488822790.005629344088070.07463630025670.330048242498-0.03250974248820.1302303791660.211235388688-0.0219130169957-0.04762188128090.1383673688130.1064349853280.2463152526363.077740295626.437270120432.7378823636
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 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 132 )
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 141 )
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 147 )

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