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- PDB-1i20: MUTANT HUMAN LYSOZYME (A92D) -

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Basic information

Entry
Database: PDB / ID: 1i20
TitleMUTANT HUMAN LYSOZYME (A92D)
ComponentsLYSOZYME C
KeywordsHYDROLASE / CALCIUM BINDING SITE / MUTANT HUMAN LYSOZYME
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: 1.9 Å
AuthorsKuroki, R.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Structural and thermodynamic responses of mutations at a Ca2+ binding site engineered into human lysozyme.
Authors: Kuroki, R. / Yutani, K.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Thermodynamic Changes in the Binding of Ca2+ to a Mutant Human Lysozyme (D86/92). Enthalpy-entropy compensation observed upon Ca2+ binding to proteins.
Authors: Kuroki, R. / Nitta, K. / Yutani, K.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Entropic Stabilization of a Mutant Human Lysozyme Induced by Calcium Binding
Authors: Kuroki, R. / Kawakita, S. / Nakamura, H. / Yutani, K.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structures of the Apo- and Holomutant Human Lysozymes with an Introduced Ca2+ Binding Site
Authors: Inaka, K. / Kuroki, R. / Kikuchi, M. / Matsushima, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Design and Creation of a Ca2+ Binding Site in Human Lysozyme to Enhance Structural Stability
Authors: Kuroki, R. / Taniyama, Y. / Seko, C. / Nakamura, H. / Kikuchi, M. / Ikehara, M.
History
DepositionFeb 5, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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)14,7651
Polymers14,7651
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.070, 60.630, 33.850
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


Mass: 14764.703 Da / Num. of mol.: 1 / Mutation: A92D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PERI8811 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AH22R-
References: UniProt: P61626, deoxyribodipyrimidine endonucleosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PHOSPHATE, SODIUM CHLORIDE, CALCIUM CHLORIDE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mMphosphate11pH6.0
220 mg/mlprotein11
32.5 M11NaCl
41.5 mM11CaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 35220 / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 10159 / Num. measured all: 32762

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing
RefinementStarting model: PDB ENTRY 2LHM

2lhm


Resolution: 1.9→8 Å / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflection
Rwork0.164 --
all0.164 8000 -
obs0.164 8000 83 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 82 1114
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01210561
X-RAY DIFFRACTIONt_angle_deg2.53914271.25
X-RAY DIFFRACTIONt_dihedral_angle_d15.8786340
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012292
X-RAY DIFFRACTIONt_gen_planes0.0121576
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0171610
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_planar_d20.012
X-RAY DIFFRACTIONt_plane_restr60.012

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