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- PDB-4xjb: X-ray structure of Lysozyme1 -

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Basic information

Entry
Database: PDB / ID: 4xjb
TitleX-ray structure of Lysozyme1
ComponentsLysozyme C
KeywordsHYDROLASE / muramidase / N-acetylmuramide glycanhydrolase
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, United States, 4items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
National Institutes of HealthGM75915 United States
National Institutes of HealthP50GM073210 United States
National Institutes of HealthU54GM094599 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Panepucci, E. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5317
Polymers14,3311
Non-polymers2006
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-56 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 79.090, 38.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.5-1 M NaCl, 50-100 mM CH3COONa, pH4.5, and 15-30% PEG 400

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11705 / % possible obs: 99.7 % / Redundancy: 8 % / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TMU

3tmu


Resolution: 1.8→39.55 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 586 5.01 %
Rwork0.1705 --
obs0.1725 11703 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 6 49 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071042
X-RAY DIFFRACTIONf_angle_d1.1081409
X-RAY DIFFRACTIONf_dihedral_angle_d12.408376
X-RAY DIFFRACTIONf_chiral_restr0.046147
X-RAY DIFFRACTIONf_plane_restr0.004186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.98120.2681420.2072701X-RAY DIFFRACTION100
1.9812-2.26780.23291440.18142743X-RAY DIFFRACTION100
2.2678-2.85710.23521450.18932753X-RAY DIFFRACTION100
2.8571-39.55450.19071550.1552920X-RAY DIFFRACTION100

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