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- PDB-1b7l: VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES -

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Entry
Database: PDB / ID: 1b7l
TitleVERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / MUTANT STABILITY / HUMAN LYSOZYME
Function / homologyGlycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Glycoside hydrolase, family 22, conserved site / Amyloid fiber formation / Antimicrobial peptides / Neutrophil degranulation / Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22 / Alpha-lactalbumin / lysozyme C family profile. ...Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Glycoside hydrolase, family 22, conserved site / Amyloid fiber formation / Antimicrobial peptides / Neutrophil degranulation / Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22 / Alpha-lactalbumin / lysozyme C family profile. / Alpha-lactalbumin / lysozyme C signature. / antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / killing of cells of other organism / lysozyme / 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 / Lysozyme C
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / 1.8 Å resolution
AuthorsTakano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K.
Citation
Journal: Protein Eng. / Year: 1999
Title: Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.
Authors: Takano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: A General Rule for the Relationship between Hydrophobic Effect and Conformational Stability of a Protein: Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozyme
Authors: Takano, K. / Yamagata, Y. / Yutani, K.
#2: Journal: Biochemistry / Year: 1998
Title: Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine->Phenylalanine Mutants
Authors: Yamagata, Y. / Kubota, M. / Sumikawa, Y. / Funahashi, J. / Takano, K. / Fujii, S. / Yutani, K.
#3: Journal: Biochemistry / Year: 1997
Title: Contribution of 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.
#4: 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.
#5: 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. / Ogasawaha, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 24, 1999 / Release: Jan 27, 1999
RevisionDateData content typeGroupProviderType
1.0Jan 27, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7862
Polyers14,7631
Non-polymers231
Water4,612256
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.480, 61.460, 32.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide PROTEIN (LYSOZYME)


Mass: 14762.773 Da / Num. of mol.: 1 / Mutation: A32L / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Saccharomyces / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 256 / Formula: H2O / Water

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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: 1.93 / Density percent sol: 36.28 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temp: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein1drop
22.5 M1reservoirNaCl
320 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Collection date: Sep 13, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 40 Å / Number obs: 30119 / Observed criterion sigma I: 1 / Rmerge I obs: 0.046 / Redundancy: 2.5 % / Percent possible obs: 90.5
Reflection shellRmerge I obs: 0.152 / Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / MeanI over sigI obs: 3.8 / Percent possible all: 77.8
Reflection
*PLUS
Number obs: 10064 / Number measured all: 30119

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLORmodel building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLORphasing
RefineMethod to determine structure: OTHER
Starting model: WILD-TYPE HUMAN LYSOZYME

Sigma F: 3
Least-squares processR factor R work: 0.174 / R factor obs: 0.174 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Number reflection obs: 9415 / Percent reflection obs: 86
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 1032 / Nucleic acid: 0 / Ligand: 1 / Solvent: 256 / Total: 1289
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
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
Refine LS shellHighest resolution: 1.8 Å / R factor R work: 0.217 / Lowest resolution: 1.88 Å / Number reflection R work: 881 / Total number of bins used: 8 / Percent reflection obs: 66.2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine
*PLUS
Sigma F: 3
Least-squares process
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
X-RAY DIFFRACTIONx_angle_deg1.60
Refine LS shell
*PLUS
Highest resolution: 1.8 Å / R factor R work: 0.217

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