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- PDB-1b5x: Contribution of hydrogen bonds to the conformational stability of... -

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Basic information

Entry
Database: PDB / ID: 1b5x
TitleContribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and x-ray analysis of six ser->ala mutants
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROGEN BOND / STABILITY
Function / homology
Function and homology information


antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of other organism / cytolysis / defense response to Gram-negative bacterium ...antimicrobial humoral response / azurophil granule lumen / specific granule lumen / retina homeostasis / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of other organism / 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
C-type lysozyme/alpha-lactalbumin family / Lysozyme C / Lysozyme-like domain superfamily / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / Lysozyme - #10 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Lysozyme C
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 Tyr->Phe 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 Valine Mutants 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. / Funahasihi, J.F. / 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. / Ogasawaha, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7282
Polymers14,7051
Non-polymers231
Water4,306239
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.360, 62.620, 32.550
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 PROTEIN (LYSOZYME)


Mass: 14704.693 Da / Num. of mol.: 1 / Mutation: SER 80 REPLACED BY ALA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEL125 / Production host: Saccharomyces cerevisiae (baker's yeast) / Strain (production host): AH22R- / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION / Sodium


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


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38 %
Crystal growpH: 4.5 / Details: 1.5M TO 1.8M NACL, 20MM ACETATE, PH 4.5
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62.
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

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 7913 / % possible obs: 95.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 8.1 / % possible all: 96.4
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 23122

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE OF HUMAN LYSOZYME

Resolution: 2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.152 --
Obs0.152 7207 89.2 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 1 239 1268
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_deg1.53
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
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.18 844 -
Obs--84.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 3
LS refinement shell
*PLUS
Rfactor Rwork: 0.18

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