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- PDB-1w08: STRUCTURE OF T70N HUMAN LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1w08
TitleSTRUCTURE OF T70N HUMAN LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / HUMAN LYSOZYME / ENZYME / AMYLOID
Function / homology
Function and homology information


cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Lysozyme C / 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 C / 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
Lysozyme C / Lysozyme C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJohnson, R. / Christodoulou, J. / Luisi, B. / Dumoulin, M. / Caddy, G. / Alcocer, M. / Murtagh, G. / Archer, D.B. / Dobson, C.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Rationalising Lysozyme Amyloidosis: Insights from the Structure and Solution Dynamics of T70N Lysozyme.
Authors: Johnson, R. / Christodoulou, J. / Dumoulin, M. / Caddy, G. / Alcocer, M. / Murtagh, G. / Kumita, J.R. / Larsson, G. / Robinson, C.V. / Archer, D.B. / Luisi, B. / Dobson, C.M.
History
DepositionJun 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7692
Polymers14,7341
Non-polymers351
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.117, 56.178, 62.488
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 / / 1 / 4-BETA-N-ACETYLMURAMIDASE C


Mass: 14733.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS 115 / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVARIANT DESCRIBED IN UNIPROT WITH FTID=VAR_012050 IN P00695

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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: 1.86 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: HANGING DROP METHOD AT 293K. DROPLET RESERVOIR SOLUTION MIXED 1:1 WITH 10 MG/ML PROTEIN, 10 MM HEPES BUFFER PH 7.5, 0.4 M LICL. RESERVOIR 2.5 M NACL, 20 MM NAOAC PH 4.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MSC / Detector: IMAGE PLATE / Date: Nov 15, 2004 / Details: OSMIC MIRROR
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 3903 / % possible obs: 95.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 6.5 / % possible all: 87.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JSF

1jsf


Resolution: 2.5→41.89 Å / SU B: 14.331 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Details: HYDROGENS ADDED IN RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26759 358 9.2 %RANDOM
Rwork0.17674 ---
obs0.18487 3529 95.08 %-
Displacement parametersBiso mean: 23.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 1 88 1119

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