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- PDB-1hc0: structure of lysozyme with periodate -

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Basic information

Entry
Database: PDB / ID: 1hc0
Titlestructure of lysozyme with periodate
ComponentsLYSOZYME C
KeywordsHYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
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
IODIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.82 Å
AuthorsOndracek, J. / Jursik, F. / Brynda, J. / Rezacova, P. / Sedlacek, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Regular Arrangement of Periodates Bound to Lysozyme.
Authors: Ondracek, J. / Weiss, M.S. / Brynda, J. / Fiala, J. / Jursik, F. / Rezacova, P. / Jenner, L.B. / Sedlacek, J.
History
DepositionApr 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 14, 2016Group: Data collection / Other
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,63612
Polymers14,3311
Non-polymers1,30411
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.765, 77.765, 37.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Number of models10
Components on special symmetry positions
IDModelComponents
11A-1109-

HOH

21A-8131-

HOH

32A-1108-

HOH

42A-8131-

HOH

53A-1108-

HOH

63A-8131-

HOH

74A-1106-

HOH

84A-8131-

HOH

95A-1103-

HOH

105A-8131-

HOH

116A-1099-

HOH

126A-8131-

HOH

137A-1098-

HOH

147A-8131-

HOH

158A-1097-

HOH

168A-8131-

HOH

179A-1097-

HOH

189A-1190-

HOH

199A-8131-

HOH

2010A-1096-

HOH

2110A-1164-

HOH

2210A-8131-

HOH

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Components

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D 4 / GAL D IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.54 Å3/Da / Density % sol: 20 %
Crystal growpH: 4.5 / Details: SOAKED AT PERIODATE, pH 4.50

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 13140 / % possible obs: 70 % / Rsym value: 0.0623 / Net I/σ(I): 5.9

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Processing

Software
NameVersionClassification
SHELXL-97refinement
HKL1998data reduction
HKLV. 1998data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.82→8 Å / Num. parameters: 4966 / Num. restraintsaints: 4268 / Cross valid method: FREE R HHSR MODIFICATION / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
all0.16 10310 --
obs--99.7 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1166.19
Refinement stepCycle: LAST / Resolution: 1.82→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 11 220 1225

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