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- PDB-1gd6: STRUCTURE OF THE BOMBYX MORI LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1gd6
TitleSTRUCTURE OF THE BOMBYX MORI LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE / BMLZ
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium
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 speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.5 Å
AuthorsMatsuura, A. / Aizawa, T. / Yao, M. / Kawano, K. / Tanaka, I. / Nitta, K.
CitationJournal: Biochemistry / Year: 2002
Title: Structural analysis of an insect lysozyme exhibiting catalytic efficiency at low temperatures.
Authors: Matsuura, A. / Yao, M. / Aizawa, T. / Koganesawa, N. / Masaki, K. / Miyazawa, M. / Demura, M. / Tanaka, I. / Kawano, K. / Nitta, K.
History
DepositionSep 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)13,7781
Polymers13,7781
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.268, 77.268, 72.925
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer

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Components

#1: Protein LYSOZYME /


Mass: 13777.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Pichia pastoris (fungus) / References: UniProt: P48816, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.957779 Å3/Da / Density % sol: 68.9623903 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 69 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium sulfate1drop
326 %(w/v)PEG80001drop
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Aug 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 55985 / Num. obs: 7862 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 7.12 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.8388 / Num. unique all: 742 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 97639
Reflection shell
*PLUS
% possible obs: 96.4 % / Redundancy: 5.08 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.84

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: molecular replacement / Resolution: 2.5→10 Å / Isotropic thermal model: RESTRAINTS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 747 9.4 %RAMDOM
Rwork0.1809 ---
all-7917 --
obs-7685 97.1 %-
Solvent computationBsol: 30.2625 Å2 / ksol: 0.358547 e/Å3
Displacement parametersBiso mean: 38.84 Å2
Baniso -1Baniso -2Baniso -3
1-5.068 Å20 Å20 Å2
2--5.068 Å20 Å2
3----10.136 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.322 Å0.27 Å
Luzzati sigma a0.51 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 64 1027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008512
X-RAY DIFFRACTIONc_angle_deg1.55289
X-RAY DIFFRACTIONc_torsion_deg23.47519
X-RAY DIFFRACTIONc_torsion_impr_deg0.73009
X-RAY DIFFRACTIONc_dihedral_angle_d23.47519
X-RAY DIFFRACTIONc_improper_angle_d0.73009
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.3059 -
Rwork0.3019 550
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.223 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.47519
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73009

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