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

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Basic information

Entry
Database: PDB / ID: 6sil
TitleSAD structure of Hen Egg White Lysozyme recovered by inverse beam geometry data collection and multivariate analysis of Friedel pairs
ComponentsLysozyme C
KeywordsHYDROLASE / Multivariate 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
Water3,189177
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 area2080 Å2
ΔGint-79 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-340-

HOH

21A-402-

HOH

31A-471-

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, 191 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.: 177 / 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: 13.62 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: 0.13287775586 / Cross valid method: FREE R-VALUE / σ(F): 0.000458515671031 / Phase error: 16.1268318032
RfactorNum. reflection% reflection
Rfree0.169342803501 1345 4.84876888136 %
Rwork0.143467876563 --
obs0.14469894543 27739 95.6451279222 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.2989554034 Å2
Refinement stepCycle: LAST / Resolution: 1.6101802385→39.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 29 177 1207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005509060692151104
X-RAY DIFFRACTIONf_angle_d0.7818815895071495
X-RAY DIFFRACTIONf_chiral_restr0.0530191814368151
X-RAY DIFFRACTIONf_plane_restr0.00407447855953200
X-RAY DIFFRACTIONf_dihedral_angle_d9.58127699747660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6102-1.66770.2182103463191100.2134457013611881X-RAY DIFFRACTION68.9165801315
1.6677-1.73450.2043599246911590.162557693752663X-RAY DIFFRACTION97.9520999653
1.7345-1.81340.2013072506861260.1602058151612761X-RAY DIFFRACTION98.7346101231
1.8134-1.90910.1923084823361350.1404069118692688X-RAY DIFFRACTION98.3966538864
1.9091-2.02870.1906896582191340.1322556203232770X-RAY DIFFRACTION98.9100817439
2.0287-2.18530.146143040571390.133345518082729X-RAY DIFFRACTION99.1358451434
2.1853-2.40520.1509409170921270.1343965558912731X-RAY DIFFRACTION98.7219343696
2.4052-2.75310.1696228058841350.1500669327182727X-RAY DIFFRACTION98.7577639752
2.7531-3.46830.165447307331400.1411805465952707X-RAY DIFFRACTION98.0709610748
3.4683-39.530.1566349875951400.1398706984122737X-RAY DIFFRACTION98.8659793814
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)
13.41171719191-3.525859580811.816868057748.15224203381-2.253475263164.63121304995-0.0439075137216-0.02141475278470.2323929661340.191337550817-0.0413280372865-0.130922431431-0.1725986370020.1674118679270.08396913785020.127288925757-0.0268958005676-0.01398647954490.102691397821-0.04256504022260.14889950033822.986566203446.252900529727.7028913811
27.093891502132.676190740330.2520372693435.323831586370.5302799395111.148369273070.1028821256870.0590060503770.4303600372090.13567408589-0.130913679110.0125848882815-0.1104348092730.07118252509390.03747241128970.1405108934770.01486811151260.001518681332480.08597384707380.02767003773990.1482849464315.65429435451.347303998315.9975367798
31.59474450076-0.888349125419-0.001131780232611.764509046360.4093053562241.55357751242-0.005763941227680.103864462937-0.1137343175710.07488805478880.02740545768510.07409441446660.134704743043-0.03971378315310.00183160142520.0675307894722-0.00726530170315-0.00686831526370.0670647892006-0.01146539976460.086124654633118.438309325834.313364558220.7435875636
47.26549241515-5.60765160861-4.076343197056.926909559083.104278843276.376174618320.06439273824060.1395189702590.116131461048-0.058575786939-0.04446923242020.0314309261509-0.22653688767-0.1226856993830.009363657782390.06874592329080.00490440127578-0.003612776474810.06153748822260.002343546645970.061712237173221.821398368534.383946477717.3603089074
55.6625405274-4.355000005822.635770965093.8081520101-2.691505368412.83532625670.3527475137250.237616753671-0.325564366-0.640553190659-0.2490369571480.1865524318560.148559717192-0.167680749174-0.1160423793720.1483350769860.0204447037086-0.008735389946140.151063593641-0.02357128393460.12112211620323.943442387830.58871311597.83267719734
61.70866089249-0.554054096308-0.4974362983123.487534536830.5722906703064.076723895410.1460328241710.1307378834820.199919885911-0.293262912129-0.151097269527-0.239883215793-0.0736291331931-0.002913410984840.006834216692460.09102836886360.02194085582230.01979062020040.1142445148890.0187004205340.13345342051327.553002425836.245623903710.8089151185
77.26069521178-1.386140958586.94274826174.36775982471-0.5593328242916.78289888532-0.09332028421640.2145045935620.220003103338-0.06658662515-0.0174322553961-0.166889377396-0.2835098464990.2402584432660.0981338395160.09974313259870.0006064369110950.04187263960140.0770214237880.01749534759620.11238011789522.321107689644.470815767312.6677648701
83.604414169660.423665720274-0.7090069225114.53067709332-3.643542140596.726582287180.02563874124530.269140608642-0.109392271434-0.205433152302-0.03631491095440.1175917473220.314525238296-0.09967693940750.01714175126850.08636582854830.006353970791-0.0001646786242420.0672047639608-0.02016245886590.1036167692669.8163949041739.398986206414.5144110586
94.683233140143.513047808283.490409410973.968847026673.010463317674.07631031792-4.96179241727E-5-0.3083364730820.557365320733-0.0231242292972-0.1176461195240.128497895854-0.448162662208-0.1829956944920.1727538538460.1550870329130.008178983632840.02554170648510.135825026624-0.05220330545940.18511728877410.662788976748.269168447328.9047197256
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 147 )

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