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- PDB-1bb6: LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOTRIOSE -

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Basic information

Entry
Database: PDB / ID: 1bb6
TitleLYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOTRIOSE
ComponentsLYSOZYME
KeywordsHYDROLASE / N-ACETYL-MURAMIDASE / UMBELLIFERONE GLYCOSIDES
Function / homology
Function and homology information


lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space
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
METHYL-UMBELLIFERTL-N-ACETYL-CHITOTRIOSE / Lysozyme C II
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / PHASES FOR NATIVE STRUCTURE / Resolution: 2 Å
AuthorsVollan, V.B. / Hough, E. / Karlsen, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme.
Authors: Vollan, V.B. / Hough, E. / Karlsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystal Structures of Three Complexes between Chito-Oligosaccharides and Lysozyme from the Rainbow Trout. How Distorted is the Nag Sugar in Site D?
Authors: Karlsen, S. / Hough, E.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refined Crystal Structure of Lysozyme from the Rainbow Trout (Oncorhynchus Mykiss)
Authors: Karlsen, S. / Eliassen, B.E. / Hansen, L.K. / Larsen, R.L. / Riise, B.W. / Smalas, A.O. / Hough, E. / Grinde, B.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0892
Polymers14,3031
Non-polymers7861
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.690, 76.690, 54.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LYSOZYME / N-ACETYL-MURAMIDASE


Mass: 14303.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus mykiss (rainbow trout) / Organ: KIDNEY / References: UniProt: P11941, lysozyme
#2: Chemical ChemComp-UMG / METHYL-UMBELLIFERTL-N-ACETYL-CHITOTRIOSE / METHYLUMBELLIFERYL CHITOTRIOSE


Mass: 785.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H47N3O18
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62 %
Crystal growpH: 10 / Details: pH 10.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Karlsen, S., (1995) Acta Crystallogr.,Sect.D, 51, 354.
PH range low: 10 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Macetate1reservoir
20.1 Mcitrate1reservoir
30.1 Mphosphate1reservoir
418 mg/mllysozyme1drop80& of typeI and 20% of type II
530-45 %satammonium sulfate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 11445 / % possible obs: 89.5 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.8 / % possible all: 42.7
Reflection
*PLUS
Num. measured all: 20088 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 42.7 %

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Processing

Software
NameVersionClassification
MADNESdata collection
SCALAdata scaling
CCP4model building
PROLSQrefinement
MADNESdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: PHASES FOR NATIVE STRUCTURE / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.271 -5 %RANDOM
Rwork0.211 ---
obs-11404 --
Displacement parametersBiso mean: 18.87 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 55 142 1196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
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_restr0.009
X-RAY DIFFRACTIONp_chiral_restr0.0280.06
X-RAY DIFFRACTIONp_singtor_nbd0.160.3
X-RAY DIFFRACTIONp_multtor_nbd0.1880.3
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
Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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