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- PDB-1lhj: ROLE OF PROLINE RESIDUES IN HUMAN LYSOZYME STABILITY: A SCANNING ... -

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Basic information

Entry
Database: PDB / ID: 1lhj
TitleROLE OF PROLINE RESIDUES IN HUMAN LYSOZYME STABILITY: A SCANNING CALORIMETRIC STUDY COMBINED WITH X-RAY STRUCTURE ANALYSIS OF PROLINE MUTANTS
ComponentsHUMAN LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


Amyloid fiber formation / Antimicrobial peptides / Neutrophil degranulation / antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / killing of cells of other organism ...Amyloid fiber formation / Antimicrobial peptides / Neutrophil degranulation / antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / killing of cells of other organism / lysozyme activity / cytolysis / defense response to Gram-negative bacterium / inflammatory response / defense response to Gram-positive bacterium / defense response to bacterium / cellular protein metabolic process / neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Glycoside hydrolase, family 22, conserved site / Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22 / Glycosyl hydrolases family 22 (GH22) domain profile. / Glycosyl hydrolases family 22 (GH22) domain signature.
Lysozyme C
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsInaka, K. / Matsushima, M. / Herning, T. / Kuroki, R. / Yutani, K. / Kikuchi, M.
Citation
Journal: Biochemistry / Year: 1992
Title: Role of proline residues in human lysozyme stability: a scanning calorimetric study combined with X-ray structure analysis of proline mutants.
Authors: Herning, T. / Yutani, K. / Inaka, K. / Kuroki, R. / Matsushima, M. / Kikuchi, M.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structures of the Apo-and Holomutant Human Lysozymes with an Introduced Ca Binding Site
Authors: Inaka, K. / Kuroki, R. / Kikuchi, M. / Matsushima, M.
#2: Journal: Biochemistry / Year: 1991
Title: Effects of Proline Mutations on the Unfolding and Refolding of Human Lysozyme: The Slow Refolding Kinitics Phase Does not Result from Proline Cis-Trans Isomerization
Authors: Herning, T. / Yutani, K. / Taniyama, Y. / Kikuchi, M.
#3: Journal: Biochemistry / Year: 1992
Title: Role of Proline Residues in Human Lysozyme Stability: A Scanning Calorimetric Study Combined with X-Ray Structure Analysis of Proline Mutants
Authors: Herning, T. / Yutani, K. / Inaka, K. / Kuroki, R. / Matsushima, M. / Kikuchi, M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 27, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,6811
Polymers14,6811
Non-polymers00
Water2,306128
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.460, 61.210, 33.840
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/peptide HUMAN LYSOZYME /


Mass: 14680.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal grow
*PLUS
Temperature: 13 ℃ / pH: 5.8 / Method: unknown
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: 1

IDConc.Common nameDetailsChemical formula
120 mg/mlprotein
22.5 MprecipitantNaCl
330 mMsodium phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 9358 / % possible obs: 82 % / Num. measured all: 39581 / Rmerge(I) obs: 0.034

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→5 Å /
RfactorNum. reflection
Obs0.152 9358
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 128 1154
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Num. reflection obs: 9358 / Rfactor obs: 0.152 / Lowest resolution: 5 Å
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_plane_restr0.014
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.89 Å / Rfactor obs: 0.187

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