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- PDB-1b5z: CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF... -

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Basic information

Entry
Database: PDB / ID: 1b5z
TitleCONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROGEN BOND / STABILITY
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / 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 / tertiary granule lumen / lysozyme / lysozyme activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTakano, K. / Yamagata, Y. / Kubota, M. / Funahashi, J. / Fujii, S. / Yutani, K.
Citation
Journal: Biochemistry / Year: 1999
Title: Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.
Authors: Takano, K. / Yamagata, Y. / Kubota, M. / Funahashi, J. / Fujii, S. / 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 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.
#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.Biochem.(Tokyo) / Year: 1996
Title: The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme
Authors: Funahashi, J. / Takano, K. / Ogasahara, K. / Yamagata, Y. / Yutani, K.
#6: 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.
History
DepositionJan 11, 1999Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)29,4092
Polymers29,4092
Non-polymers00
Water2,468137
1
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,7051
Polymers14,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,7051
Polymers14,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.670, 110.300, 43.640
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


Mass: 14704.693 Da / Num. of mol.: 2 / Mutation: S82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEL125 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AH22R- / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.6 Å3/Da / Density % sol: 54 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 M1reservoirNaCl
320 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→100 Å / Num. obs: 23175 / % possible obs: 79.4 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.81→1.9 Å / Mean I/σ(I) obs: 2.4 / % possible all: 52.6
Reflection
*PLUS
Num. measured all: 68449
Reflection shell
*PLUS
% possible obs: 52.6 %

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I56F MUTANT HUMAN LYSOZYME

Resolution: 2.2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.148 --
obs0.148 14157 88 %
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 257 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.48
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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