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- PDB-4n0j: Crystal structure of dimethyllysine hen egg-white lysozyme in com... -

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Basic information

Entry
Database: PDB / ID: 4n0j
TitleCrystal structure of dimethyllysine hen egg-white lysozyme in complex with sclx4 at 1.9 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: 1.9 Å
AuthorsMcGovern, R.E. / 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
DepositionOct 2, 2013Deposition 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,66017
Polymers29,0432
Non-polymers3,61715
Water3,441191
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3709
Polymers14,5211
Non-polymers1,8498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2908
Polymers14,5211
Non-polymers1,7697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 30.200, 94.210
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 206 molecules

#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293.15 K / pH: 6.1
Details: 6 % PEG 8000, 100 mM, MAGNESIUM CHLORIDE, 50 mM SODIUM CHLORIDE, 100 mM SODIUM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 198.8 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.674→31.22 Å / Num. all: 30169 / Num. obs: 27755 / % possible obs: 92 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.8
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.026 / Mean I/σ(I) obs: 1.1 / % possible all: 86.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IPQ

4ipq
PDB Unreleased entry


Resolution: 1.9→31.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.16 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1008 5.1 %RANDOM
Rwork0.168 ---
obs0.17 18582 94.6 %-
all-19591 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.2 Å2
2---0.53 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 228 191 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.8523285
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61223.208106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97515299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6191523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021817
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_it0.7441.2331052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2721.8411317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9831.4531340
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 76 -
Rwork0.214 1270 -
obs--90.03 %

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