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- PDB-2zwb: Neutron crystal structure of wild type human lysozyme in D2O -

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Basic information

Entry
Database: PDB / ID: 2zwb
TitleNeutron crystal structure of wild type human lysozyme in D2O
ComponentsLysozyme C
KeywordsHYDROLASE / NEUTRON D2O HYDROGEN HYDRATION / Amyloid / Amyloidosis / Antimicrobial / Bacteriolytic enzyme / Disease mutation / Glycosidase
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
DEUTERATED WATER / Lysozyme C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChiba-Kamoshida, K. / Matsui, T. / Chatake, T. / Ohhara, T. / Ostermann, A. / Tanaka, I. / Yutani, K. / Niimura, N.
CitationJournal: To be Published
Title: Site-specific softening of peptide bonds by localized deuterium observed by neutron crystallography of human lysozyme
Authors: Chiba-Kamoshida, K. / Matsui, T. / Chatake, T. / Ohhara, T. / Ostermann, A. / Tanaka, I. / Yutani, K. / Niimura, N.
History
DepositionDec 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,7211
Polymers14,7211
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.825, 56.883, 60.965
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: small tubes / pH: 4.3 / Details: PH 4.30(PD), SMALL TUBES, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Type: OTHER / Wavelength: 2.88 Å
DetectorType: JAERI BIX-3 / Detector: IMAGE PLATE / Date: Jul 1, 2001
RadiationMonochromator: ELASTICALLY-BENT PERFECT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.88 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 25514 / Num. obs: 25514 / % possible obs: 69 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.211 / Χ2: 1.107 / Net I/σ(I): 3.894
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.11 / Χ2: 1.119

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.006data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FE0

3fe0


Resolution: 1.8→20 Å / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.247 1089 9.6 %
Rwork0.223 --
obs0.223 10947 96.1 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso max: 72.49 Å2 / Biso mean: 10.298 Å2 / Biso min: 3.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 65 1094
Xplor file
Refine-IDSerial noParam file
NEUTRON DIFFRACTION1protein_kc4.paramdefhardnlys
NEUTRON DIFFRACTION2parneutron.solkc3

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