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- PDB-1ckg: T52V MUTANT HUMAN LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1ckg
TitleT52V MUTANT HUMAN LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / STABILITY / HYDROGEN BOND
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTakano, K. / Yamagata, Y. / Funahashi, J. / Yutani, K.
CitationJournal: Biochemistry / Year: 1999
Title: Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,).
Authors: Takano, K. / Yamagata, Y. / Funahashi, J. / Hioki, Y. / Kuramitsu, S. / Yutani, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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: PROTEIN (LYSOZYME)
B: PROTEIN (LYSOZYME)


Theoretical massNumber of molelcules
Total (without water)29,4372
Polymers29,4372
Non-polymers00
Water5,459303
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)65.257, 106.667, 39.542
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: 14718.719 Da / Num. of mol.: 2 / Mutation: T52V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
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: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16216 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.3 / % possible all: 61.1
Reflection
*PLUS
Num. measured all: 31949
Reflection shell
*PLUS
% possible obs: 61.1 %

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
AMoREphasing
X-PLOR3.1refinement
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE OF HUMAN LYSOZYME

Resolution: 2.2→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.166 --
Obs-11543 81.5 %
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 303 2361
Refine LS restraints
Refinement-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_deg1.563
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.305
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→2.29 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.239 1397 -
Obs--80.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.305

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