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- PDB-1io5: HYDROGEN AND HYDRATION OF HEN EGG-WHITE LYSOZYME DETERMINED BY NE... -

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Basic information

Entry
Database: PDB / ID: 1io5
TitleHYDROGEN AND HYDRATION OF HEN EGG-WHITE LYSOZYME DETERMINED BY NEUTRON DIFFRACTION
ComponentsLYSOZYME C
KeywordsHYDROLASE / HYDROGEN / HYDRATION
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
DEUTERATED WATER / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiimura, N. / Minezaki, Y. / Nonaka, T. / Castagna, J.C. / Cipriani, F. / Hoeghoej, P. / Lehmann, M.S. / Wilkinson, C.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.
Authors: Niimura, N. / Minezaki, Y. / Nonaka, T. / Castagna, J.C. / Cipriani, F. / Hoghoj, P. / Lehmann, M.S. / Wilkinson, C.
#1: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1999
Title: Neutrons expand the field of structural biology
Authors: Niimura, N.
History
DepositionJan 14, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Oct 25, 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

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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)14,3311
Polymers14,3311
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.800, 80.800, 37.100
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-306-

DOD

21A-362-

DOD

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Components

#1: Protein LYSOZYME C


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: D2O

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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: 291 K / Method: concentration gradient method / pH: 7
Details: NiCl2, pH 7.0, concentration gradient method, temperature 291K

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Data collection

Diffraction sourceSource: NUCLEAR REACTOR / Wavelength: 2.9-4.0
DetectorType: LADI / Detector: IMAGE PLATE / Date: Sep 3, 1995
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.91
241
ReflectionResolution: 2→8.94 Å / Num. obs: 6700 / % possible obs: 81.4 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.164
Reflection shellResolution: 2→2.48 Å / % possible all: 77.1

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Processing

Software
NameVersionClassification
CCP4LAUE SUITE MODIFIED FOR CYLINDER GEOMETRY (C. WILKINSON)refinement
INTLDMdata reduction
X-PLORmodel building
X-PLOR3.851refinement
CCP4LAUE SUITE MODIFIED FOR CYLINDER GEOMETRY (C. WILKINSON)data reduction
INTLDMdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 193L

193l


Resolution: 2→8.94 Å / σ(I): 1
RfactorNum. reflectionSelection details
Rfree0.323 -RANDOM
obs0.21 6700 -
Refinement stepCycle: LAST / Resolution: 2→8.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 251 1252
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg2.22

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