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- PDB-2heb: CONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO T... -

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Basic information

Entry
Database: PDB / ID: 2heb
TitleCONTRIBUTION OF WATER MOLECULES IN THE INTERIOR OF A PROTEIN TO THE CONFORMATIONAL STABILITY
ComponentsLYSOZYME
KeywordsHYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME
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 / defense response to Gram-positive bacterium / inflammatory response / 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 / Alpha-lactalbumin / lysozyme C family profile. / Alpha-lactalbumin / lysozyme C signature.
Lysozyme C
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTakano, K. / Funahashi, J. / Yamagata, Y. / Fujii, S. / Yutani, K.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Contribution of water molecules in the interior of a protein to the conformational stability.
Authors: Takano, K. / Funahashi, J. / Yamagata, Y. / Fujii, S. / Yutani, K.
#1: Journal: Biochemistry / Year: 1997
Title: Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants
Authors: Takano, K. / Yamagata, Y. / Fujii, S. / Yutani, K.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
Authors: Takano, K. / Ogasahara, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)14,7022
Polymers14,6791
Non-polymers231
Water4,143230
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.800, 61.220, 33.760
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 LYSOZYME /


Mass: 14678.613 Da / Num. of mol.: 1 / Mutation: I23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN LYSOZYME WITH ILE 23 REP / Plasmid: PERI8602
Gene (production host): HUMAN LYSOZYME WITH ILE 23 REPLACED BY ALA
Production host: Saccharomyces cerevisiae (baker's yeast) / Strain (production host): AH22R- / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Sodium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2 Å3/Da / Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Takano, K., (1997) Biochemistry, 36, 688.
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
110 mg/mlproteindrop
22.5 MreservoirNaCl
320 mMacetatereservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Dec 7, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 5702 / % possible obs: 67.7 % / Observed criterion σ(I): 1 / Redundancy: 3.87 % / Rmerge(I) obs: 0.071
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 21591
Reflection shell
*PLUS
% possible obs: 56.2 % / Rmerge(I) obs: 0.185

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.124 --
Obs0.124 4109 66.3 %
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 232 1258
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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