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- PDB-1at5: HEN EGG WHITE LYSOZYME WITH A SUCCINIMIDE RESIDUE -

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Basic information

Entry
Database: PDB / ID: 1at5
TitleHEN EGG WHITE LYSOZYME WITH A SUCCINIMIDE RESIDUE
ComponentsLYSOZYME
KeywordsHYDROLASE / SUCCINIMIDE / O-GLYCOSYL HYDROLASE
Function / homology
Function and homology information


catabolism by organism of cell wall peptidoglycan in other organism / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of other organism / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...catabolism by organism of cell wall peptidoglycan in other organism / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of other organism / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNoguchi, S. / Miyawaki, K. / Satow, Y.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose.
Authors: Noguchi, S. / Miyawaki, K. / Satow, Y.
#1: Journal: J.Cryst.Growth / Year: 1996
Title: Crystallography of Succinimide Hen Egg-White Lysozyme at Low Temperatures
Authors: Miyawaki, K. / Noguchi, S. / Harada, S. / Satow, Y.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 18, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0196
Polymers14,2971
Non-polymers7225
Water1,71195
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)78.610, 78.610, 38.780
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-142-

HOH

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Components

#1: Protein/peptide LYSOZYME /


Mass: 14297.145 Da / Num. of mol.: 1 / Details: SUCCINIMIDE AT RESIDUE 101 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#3: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.2
Details: CRYSTALS WERE PREPARED AT 277K FROM A SOLUTION CONTAINING 20 MG/ML PROTEIN, 7 MM TRI-N-ACETYLCHITOTRIOSE, 25 MG/ML SODIUM CHLORIDE, AND 100 MM ACETATE BUFFER PH 4.2, BY EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION CONTAINING 50 MG/ML SODIUM CHLORIDE AND 100 MM ACETATE BUFFER PH 4.2.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
120 mg/mlproteindrop
27 mMNAG3drop
3430 mMdropNaCl
4100 mMsodium acetatedrop
5860 mMreservoirNaCl
6100 mMsodium acetatereservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.8 Å / Num. obs: 10924 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.8→1.83 Å / % possible all: 65.2
Reflection
*PLUS
Num. measured all: 56262
Reflection shell
*PLUS
% possible obs: 65.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZB
Resolution: 1.8→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ALTHOUGH BOND DISTANCE BETWEEN ILE 98 CB AND CA DEVIATES BY LARGER THAN 4.0*RMSD FROM THE IDEAL VALUE, ALL THE ATOMS OF ILE 98 ARE DEFINED IN CLEAR ELECTRON DENSITIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1071 10 %RANDOM
Rwork0.182 ---
Obs0.182 10754 92.8 %-
Displacement parametersBiso mean: 20.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 45 95 1140
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg1.35
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d23
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d1.28
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it1.541.5
x_mcangle_it2.442
x_scbond_it2.932
x_scangle_it4.612.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 89 10 %
Rwork0.233 668 -
Obs--65.2 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PARHCSDX.PROTOPHCSDX.PRO
2PARAM19X.SOLTOPH19.SOL
3PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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