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- PDB-1n4f: Para-Arsanilate Derivative of Hen Egg-White Lysozyme -

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Basic information

Entry
Database: PDB / ID: 1n4f
TitlePara-Arsanilate Derivative of Hen Egg-White Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE
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
4-AMINOPHENYLARSONIC ACID / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsRetailleau, P. / Prange, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Phasing power at the K absorption edge of organic arsenic.
Authors: Retailleau, P. / Prange, T.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,31610
Polymers14,3311
Non-polymers9849
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.764, 76.764, 38.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

21A-321-

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 / Details: hen egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ASR / 4-AMINOPHENYLARSONIC ACID / Arsanilic acid


Mass: 217.054 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8AsNO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.7 Å3/Da / Density % sol: 26.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 250 mM sodium para-arsanilate then transferred to equivalent solution plus 15% V/V ethyleneglycol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein1drop
2100 mMcacodylate1droppH6.5
3250 mMsodium para-arsanilate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.0438 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2002
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0438 Å / Relative weight: 1
ReflectionResolution: 1.78→15.66 Å / Num. obs: 11331 / % possible obs: 99.4 % / Redundancy: 13.7 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.054 / Net I/σ(I): 8.5
Reflection shellResolution: 1.78→1.87 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1459 / Rsym value: 0.165 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 15.7 Å / Num. obs: 11323 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.165

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
BUSTER-TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.78→15.66 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1113 -random
Rwork0.164 ---
all0.169 11490 --
obs-11330 99.5 %-
Refine analyzeLuzzati coordinate error obs: 0.162 Å
Refinement stepCycle: LAST / Resolution: 1.78→15.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 54 121 1186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.212
X-RAY DIFFRACTIONt_dihedral_angle_d14.6
LS refinement shellResolution: 1.78→1.82 Å
RfactorNum. reflection% reflection
Rfree0.223 156 -
Rwork0.176 --
obs-1614 10 %
Software
*PLUS
Name: BUSTER-TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 16 Å / Num. reflection all: 11331 / Num. reflection obs: 10217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg23.2

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