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- PDB-1qsw: CRYSTAL STRUCTURE ANALYSIS OF A HUMAN LYSOZYME MUTANT W64C C65A -

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Basic information

Entry
Database: PDB / ID: 1qsw
TitleCRYSTAL STRUCTURE ANALYSIS OF A HUMAN LYSOZYME MUTANT W64C C65A
ComponentsHUMAN LYSOZYME MUTANT
KeywordsHYDROLASE
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / Resolution: 1.85 Å
AuthorsInaka, K. / Kanaya, E. / Kikuchi, M. / Miki, K.
CitationJournal: Proteins / Year: 2001
Title: Crystal structure of a mutant human lysozyme with a substituted disulfide bond.
Authors: Inaka, K. / Kanaya, E. / Kikuchi, M. / Miki, K.
History
DepositionJun 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN LYSOZYME MUTANT
B: HUMAN LYSOZYME MUTANT
C: HUMAN LYSOZYME MUTANT
D: HUMAN LYSOZYME MUTANT


Theoretical massNumber of molelcules
Total (without water)58,4224
Polymers58,4224
Non-polymers00
Water4,179232
1
A: HUMAN LYSOZYME MUTANT


Theoretical massNumber of molelcules
Total (without water)14,6061
Polymers14,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HUMAN LYSOZYME MUTANT


Theoretical massNumber of molelcules
Total (without water)14,6061
Polymers14,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HUMAN LYSOZYME MUTANT


Theoretical massNumber of molelcules
Total (without water)14,6061
Polymers14,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HUMAN LYSOZYME MUTANT


Theoretical massNumber of molelcules
Total (without water)14,6061
Polymers14,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.92, 107.24, 32.08
Angle α, β, γ (deg.)98.59, 110.45, 78.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HUMAN LYSOZYME MUTANT


Mass: 14605.561 Da / Num. of mol.: 4 / Mutation: W64C, C65A / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61626
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: SODIUM PHOSPHATE, NACL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
230 mMsodium phosphate12
32.5 M12NaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE DIP100S / Detector: IMAGE PLATE / Date: Feb 12, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→16 Å / Num. all: 76633 / Num. obs: 43715 / % possible obs: 80.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.85→1.94 Å / % possible all: 63.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 76633 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 64.3 % / Num. unique obs: 3092 / Num. measured obs: 6244 / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
ELMSdata collection
PROTEINdata reduction
X-PLORmodel building
PROLSQrefinement
ELMSdata reduction
PROTEINdata scaling
X-PLORphasing
RefinementResolution: 1.85→10 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.261 1651 RANDOM
Rwork0.181 --
all-33187 -
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 0 232 4312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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