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- PDB-1iwv: Crystal Structure Analysis of Human lysozyme at 147K. -

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Basic information

Entry
Database: PDB / ID: 1iwv
TitleCrystal Structure Analysis of Human lysozyme at 147K.
ComponentsLYSOZYME C
KeywordsHYDROLASE / O-GLYCOSYL / GLYCOSYDASE
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / 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 / lysozyme / lysozyme activity / tertiary granule lumen / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsJoti, Y. / Nakasako, M. / Kidera, A. / Go, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors.
Authors: Joti, Y. / Nakasako, M. / Kidera, A. / Go, N.
History
DepositionJun 3, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8274
Polymers14,7211
Non-polymers1063
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.219, 61.039, 33.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: pERI8602 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: NaCl, acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃ / Details: Takano, K., (1995) J. Mol. Biol., 254, 62.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 M1reservoirNaCl
320 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 147 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 24643 / Num. obs: 24634
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 95.9 % / Num. measured all: 236842 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.37 Å / % possible obs: 58.7 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 8.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
NMREFrefinement
RefinementResolution: 1.4→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.197 1126
Rwork0.16 -
obs-22546
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 3 308 2416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_bond_d0.011
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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