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- PDB-4pru: Crystal structure of dimethyllysine hen egg-white lysozyme in com... -

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Basic information

Entry
Database: PDB / ID: 4pru
TitleCrystal structure of dimethyllysine hen egg-white lysozyme in complex with sclx4 at 2.2 A resolution
ComponentsLysozyme C
KeywordsHYDROLASE / HYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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-T3Y / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcGovern, R.E. / Lyons, J.A. / Crowley, P.B.
CitationJournal: Chem Sci / Year: 2015
Title: Structural study of a small molecule receptor bound to dimethyllysine in lysozyme.
Authors: McGovern, R.E. / Snarr, B.D. / Lyons, J.A. / McFarlane, J. / Whiting, A.L. / Paci, I. / Hof, F. / Crowley, P.B.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2068
Polymers29,0432
Non-polymers3,1636
Water1,74797
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1955
Polymers14,5211
Non-polymers1,6744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0113
Polymers14,5211
Non-polymers1,4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.040, 30.280, 95.010
Angle α, β, γ (deg.)90.00, 96.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14521.488 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H24O16S4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18 % PEG 8000 100 mM MAGNESIUM CHLORIDE, 50 mM SODIUM CHLORIDE, 50 mM SODIUM CACODYLATE PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03319 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.2→39.41 Å / Num. all: 13612 / Num. obs: 13557 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.155 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 3.7 / Num. unique all: 967 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pqr

4pqr


Resolution: 2.2→39.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.13 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 670 4.9 %RANDOM
Rwork0.18004 ---
all0.349 13557 --
obs0.18288 12880 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.2 Å2
2---0.34 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 204 97 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022307
X-RAY DIFFRACTIONr_bond_other_d0.0470.028
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.8443185
X-RAY DIFFRACTIONr_angle_other_deg1.385316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00123.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66115286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 55 -
Rwork0.236 898 -
obs--98.65 %

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