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- PDB-6pbb: Crystal structure of Hen Egg White Lysozyme in complex with I3C -

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Basic information

Entry
Database: PDB / ID: 6pbb
TitleCrystal structure of Hen Egg White Lysozyme in complex with I3C
ComponentsLysozyme
KeywordsHYDROLASE
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
Chem-I3C / Lysozyme C / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89151078799 Å
AuthorsTruong, J.Q.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150103009 Australia
Australian Research Council (ARC)DP160101450 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68.
Authors: Truong, J.Q. / Panjikar, S. / Shearwin-Whyatt, L. / Bruning, J.B. / Shearwin, K.E.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6026
Polymers14,3311
Non-polymers2,2715
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 77.160, 38.201
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-326-

HOH

21A-372-

HOH

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Components

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, UniProt: P00698*PLUS, lysozyme
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4I3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.98 Å3/Da / Density % sol: 38 % / Description: Rectangular prism
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.459 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.87→38.2 Å / Num. obs: 9810 / % possible obs: 98.4 % / Redundancy: 43.7 % / Biso Wilson estimate: 26.8218497582 Å2 / Net I/σ(I): 23
Reflection shellResolution: 1.87→1.92 Å / Num. unique obs: 475

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Processing

Software
NameVersionClassification
PHENIXdev_2689refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89151078799→34.5070010288 Å / SU ML: 0.243569862865 / Cross valid method: FREE R-VALUE / σ(F): 1.90937325444 / Phase error: 27.2332016465
RfactorNum. reflection% reflection
Rfree0.240338619954 1660 9.54461821527 %
Rwork0.196642865377 --
obs0.200725274419 9547 98.717221024 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.3201983581 Å2
Refinement stepCycle: LAST / Resolution: 1.89151078799→34.5070010288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 65 73 1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003060989389291093
X-RAY DIFFRACTIONf_angle_d0.5385820908661491
X-RAY DIFFRACTIONf_chiral_restr0.0380168209544145
X-RAY DIFFRACTIONf_plane_restr0.00281873592064193
X-RAY DIFFRACTIONf_dihedral_angle_d13.4261499499624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8915-1.94720.4201276372271340.3674862782951277X-RAY DIFFRACTION95.9211420802
1.9472-2.010.3301875772341380.2366009727461326X-RAY DIFFRACTION98.3870967742
2.01-2.08180.237035098961260.1937818732561309X-RAY DIFFRACTION99.4455994456
2.0818-2.16520.2579358428051420.1855067431371317X-RAY DIFFRACTION99.590443686
2.1652-2.26370.2979578949071600.2011029270631287X-RAY DIFFRACTION96.6599866399
2.2637-2.3830.2859154707581450.1996229713841274X-RAY DIFFRACTION97.9296066253
2.383-2.53230.2981288583621580.2056377730181300X-RAY DIFFRACTION99.4542974079
2.5323-2.72770.2740291485371210.2067830447171330X-RAY DIFFRACTION99.3835616438
2.7277-3.00210.2321022779051150.2245990780261344X-RAY DIFFRACTION99.2517006803
3.0021-3.43620.2501013663211280.1999597743291337X-RAY DIFFRACTION99.6598639456
3.4362-4.32790.1864391503251460.1533685935631316X-RAY DIFFRACTION99.9316473001
4.3279-34.51270.1907981312581470.1885882426071315X-RAY DIFFRACTION99.388171312
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)
14.88076883414-1.68185720436-0.898492599474.11577338428-0.3771188636013.99573035082-0.103937958999-0.0646072320797-0.486068641772-0.01160946323540.1075967224160.1762089631740.111543348878-0.2232824368740.03356895013810.185164295332-0.01253085840120.01471792411680.2283347239120.06880735906130.2726543781420.8973073143-7.3978507502323.2454487881
23.90820877121-0.337483852579-1.921659620234.20614023002-1.133363416488.687384965380.2097669374440.3358611236140.118461411586-0.233937356662-0.0171460970763-0.0555386302857-0.4468863673810.127460190701-0.2325551576130.1934523331460.02528752721320.005147607909280.2452978005090.03998525048610.22841483134617.01677285867.5631013931518.7029852752
35.61366340732-4.398993515951.601790975036.474741575051.184249269982.422895911630.2598896277920.359930401655-0.589224416942-0.524829061935-0.2826501940030.262460192989-0.07380368821380.08115660537120.02042084074180.2320973524370.018196831778-0.03255176742230.275625924833-0.02531087206620.28006016442613.56045633161.7214354624610.7496286387
43.08480118748-0.446232055463-0.8073598361777.964812614855.354974543553.706317295720.1021683598630.3982961863020.116381034178-0.4497120499750.148463263414-0.227353525395-0.5404883550.0940524707777-0.2916164637810.2564723559720.00116905166379-4.75375919086E-50.2725070325630.04362380636410.28750492523128.7151554382-0.38144328114715.1308820022
53.977427198474.30609515215-4.56306868145.27978620293-4.665413308587.03736173886-0.345449902379-0.44283603462-1.121268675670.0284285202959-0.0483347359414-0.3704268233920.761563361210.2919523986270.5667421256160.4106292341160.04667726930470.02558152262920.3715093834860.1043358498340.43544162046728.1987726517-8.8325869060929.290795306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 129 )

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