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- PDB-1lmc: THE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN BULGECIN, A BACTERIAL ... -

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Basic information

Entry
Database: PDB / ID: 1lmc
TitleTHE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN BULGECIN, A BACTERIAL METABOLITE, AND LYSOZYME FROM THE RAINBOW TROUT
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
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
BULGECIN A / Lysozyme C II
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKarlsen, S. / Hough, E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a complex between bulgecin, a bacterial metabolite, and lysozyme from the rainbow trout.
Authors: Karlsen, S. / Hough, E.
#1: Journal: To be Published
Title: The Crystal Structures of Three Complexes between Chitooligosaccharides and Lysozyme from the Rainbow Trout
Authors: Karlsen, S. / Hough, E.
#2: Journal: To be Published
Title: The Refined Crystal Structure of Lysozyme from Rainbow Trout (Oncorhynchus Mykiss)
Authors: Karlsen, S. / Eliassen, B.E. / Hansen, L.K. / Larsen, R.L. / Riise, B.W. / Smalaas, A.O. / Hough, E. / Grinde, B.
#3: Journal: Tetrahedron / Year: 1984
Title: Structures of Bulgecins, Bacterial Metabolites with Bulge-Inducing Activity
Authors: Shinagawa, S. / Kasahara, F. / Wada, Y. / Harada, S. / Asai, M.
History
DepositionNov 14, 1994Processing site: BNL
Revision 1.0Jan 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _struct_conn.pdbx_dist_value / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)14,8552
Polymers14,3031
Non-polymers5521
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.570, 76.570, 54.400
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 / MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE


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-BUL / BULGECIN A


Mass: 551.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H29N3O14S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlbulgecin1drop
230-45 %satammonium sulfate1drop
30.1 Macetate1reservoir
40.1 Mcitrate1reservoir
50.1 Mphosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 17, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10895 / % possible obs: 86.1 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 14.68 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
MADNESdata collection
PROLSQrefinement
MADNESdata reduction
RefinementResolution: 2→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.163 10895
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 35 110 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0810.05
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_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.0410.06
X-RAY DIFFRACTIONp_singtor_nbd0.1970.03
X-RAY DIFFRACTIONp_multtor_nbd0.1850.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2770.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.43
X-RAY DIFFRACTIONp_staggered_tor18.515
X-RAY DIFFRACTIONp_orthonormal_tor17.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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