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- PDB-6sim: SAD structure of Hen Egg White Lysozyme recovered by inverse beam... -

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Basic information

Entry
Database: PDB / ID: 6sim
TitleSAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and univariate analysis
ComponentsLysozyme C
KeywordsHYDROLASE / Univariate analysis / Single-wavelength X-ray Anomalous Diffraction / Inverse beam geometry collection / 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
Revision 1.2Oct 16, 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
Water2,882160
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 area6490 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-342-

HOH

21A-366-

HOH

31A-457-

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, 174 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.: 160 / 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: 1.75 Å3/Da / Density % sol: 29.7 %
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: 28213 / % possible obs: 97.3 % / Redundancy: 38.1 % / Biso Wilson estimate: 14.0864930778 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 44.83
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.19 / Num. unique obs: 1392 / CC1/2: 0.915 / % possible all: 65.7

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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: 0.170732220944 / Cross valid method: FREE R-VALUE / σ(F): 0.54672053736 / Phase error: 18.5346495603
RfactorNum. reflection% reflection
Rfree0.17376946995 1415 5.01595179015 %
Rwork0.145960963542 --
obs0.147399816682 28210 97.2691538515 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.9213345266 Å2
Refinement stepCycle: LAST / Resolution: 1.6101802385→39.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 29 160 1190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005489457158311088
X-RAY DIFFRACTIONf_angle_d0.7793036579791468
X-RAY DIFFRACTIONf_chiral_restr0.0519751592954149
X-RAY DIFFRACTIONf_plane_restr0.0042038380808194
X-RAY DIFFRACTIONf_dihedral_angle_d9.55977429929649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6102-1.66770.3580972819731070.2780297327472004X-RAY DIFFRACTION73.0702665282
1.6677-1.73450.2307392381631450.1854032626522722X-RAY DIFFRACTION99.5140576189
1.7345-1.81340.2081089913141440.1614386543242780X-RAY DIFFRACTION100
1.8134-1.90910.1886380861231460.1424313671172723X-RAY DIFFRACTION100
1.9091-2.02870.1967472681151440.1337279695132792X-RAY DIFFRACTION100
2.0287-2.18530.1587881490931460.1375677438452751X-RAY DIFFRACTION100
2.1853-2.40520.1536841880711420.1337561064532753X-RAY DIFFRACTION100
2.4052-2.75310.1949291981851490.152638995952749X-RAY DIFFRACTION100
2.7531-3.46830.1432210641631470.1391548769582756X-RAY DIFFRACTION100
3.4683-39.530.1546946519171450.1373368950612765X-RAY DIFFRACTION100
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)
16.677140953662.94725375788-0.5181818985673.035772588021.640058741395.969627650860.00551004184332-0.2825627378720.226165264475-0.0456273921333-0.1487862023080.236705949294-0.158190300681-0.1913960412770.1032418966790.1114063406660.02937274659670.0320118889040.115771511219-0.01871281972870.16535077965133.334935866523.411754001718.4931618975
26.21960646278-2.97990303244-0.7426089807486.93459606218-0.7805094710931.67548892036-0.164017940524-0.115517293657-0.0921229826982-0.02951480815040.2206096706820.437058263167-0.0625207766928-0.1131884740760.0007287899739610.0782061356569-0.0141011636308-0.02598395620090.1458039283480.002091281164770.16112890144228.018301668916.0397499627.24474480139
31.898378648811.19581619877-0.4054465861961.885216210050.1538288998071.879466368730.0129527649954-0.0998520970453-0.0608863250033-0.109105816969-0.0103139585629-0.1010549089870.05530259924330.1496518380930.006156326253590.08445001648050.01623150282890.01432514014840.0722129329089-0.001417838994830.10572770553845.045130219318.485643393311.4104613267
48.377694030566.59367207959-1.99652020658.24141005657-4.049813313295.90425420827-0.02767653100360.0576559896766-0.00374863201579-0.1420235434970.09039209734680.14437264060.161738231889-0.232997794555-0.01990044822860.0689441813418-0.00122356261459-0.007401680289680.0822359289674-0.002860607616160.071442071376945.194625353421.80352205957.53973179455
53.891340259324.611054549423.054447199016.263233266813.153476348763.60465657873-0.2804513873770.662732848071-0.146108530147-0.2873662546360.345416148237-0.3159707247970.1932776300690.209443046998-0.1161608709170.144218858173-0.01863431629710.02612083814240.154368579748-0.008607556739740.12134475518448.494015441123.9477992235-1.40962473221
64.022856879670.706627675673-1.839523820741.11611116781-0.59317053695.38599838569-0.124912579410.2621775430340.232129129957-0.1276591211480.1425595149170.1842271496790.00813070276286-0.0765258102165-0.01129733072530.122710321448-0.0263517254883-0.02398605036360.09187478620430.01776232785070.15009685682342.710379991127.69654531741.97875932659
74.747452058841.372272506911.031767412376.490315993897.375932006568.466018538450.02384353782880.1488734292790.164566337738-0.15225676069-0.103925744860.16540634667-0.236654385767-0.3419599186940.0565108704160.09031984847790.000510567563959-0.01164119618380.1094576554470.04802338119340.13488671783834.604035261222.32785731963.42586831588
86.62171583747-1.170132300155.476461051052.97794688323-1.23399594977.847254228830.01571730799180.199593400499-0.170789436318-0.2501659366980.00780258185123-0.118573353450.152030283220.42331085720.000502613159580.0757052308417-0.009341024750930.02285949389650.0851188765362-0.003006824971070.11764519062339.67066194359.819267324175.26466171617
93.21172727574-3.31869940318-3.134022138975.087713166424.851501725224.72080215073-0.1308749483390.0160834083446-0.1616082165590.252243976539-0.004553523605560.3752123925770.330100204413-0.4729432883990.2071198463290.1334232691-0.02202869510090.01902272042070.1355946272980.02085398280890.14308150874634.24531924147.1640013675516.8982976373
107.82371230655-4.90058365222-3.580316344124.402244470654.355379685274.98802881008-0.130699883422-0.207878298513-0.3271647387380.552324064772-0.07785479897270.9467694861780.117391911402-0.2899626642760.1391171310410.2014539197950.03001297598640.118194350350.2583850516520.04562255426950.33663459111526.448918827916.001890943923.4977887509
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 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 141 )
10X-RAY DIFFRACTION10chain 'A' and (resid 142 through 147 )

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