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- PDB-3ayq: Crystal structure of inhibitor bound lysozyme from Meretrix lusoria -

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Basic information

Entry
Database: PDB / ID: 3ayq
TitleCrystal structure of inhibitor bound lysozyme from Meretrix lusoria
ComponentsLysozyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / I-type lysozyme / Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chitinase activity / metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Invertebrate-type lysozyme / Destabilase / Invertebrate (I)-type lysozyme domain profile. / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMeretrix lusoria (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsYoneda, K. / Kuwano, Y. / Usui, T. / Ogata, M. / Suzuki, A. / Araki, T.
CitationJournal: To be Published
Title: Crystal structure of inhibitor bound lysozyme from Meretrix lusoria
Authors: Yoneda, K. / Kuwano, Y. / Usui, T. / Ogata, M. / Suzuki, A. / Araki, T.
History
DepositionMay 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,1952
Polymers13,3851
Non-polymers8111
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.123, 42.123, 122.856
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-180-

HOH

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Components

#1: Protein Lysozyme / I-type lysozyme / 1 / 4-beta-N-acetylmuramidase


Mass: 13384.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meretrix lusoria (invertebrata) / References: UniProt: P86383, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-[(5S,6R)-5-hydroxy-6-(hydroxymethyl)-2-oxo-5,6-dihydro-2H-pyran-3-yl]acetamide


Type: oligosaccharide / Mass: 810.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[AZz22h_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-3-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR (2,3-DIDEOXY-N,N',N'',N'''-TETRAACETYLCHITOTETRAOSE-1,5-LACTONE) IS COMPOSED OF SUGAR ...THE INHIBITOR (2,3-DIDEOXY-N,N',N'',N'''-TETRAACETYLCHITOTETRAOSE-1,5-LACTONE) IS COMPOSED OF SUGAR RESIDUES NAG 123, NAG 124, NAG 125, AND 4NN 126.
Sequence detailsRESIDUE I5T IS NATURAL VARIANT ACCORDING TO REFERENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT P86383 (LYS_MERLU).

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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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 35% 2-propanol, 0.1M Citrate buffer (pH5.5), 5% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 11424 / Biso Wilson estimate: 12.5 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AB6

3ab6


Resolution: 1.77→24.09 Å /
RfactorNum. reflection
Rfree0.231 -
Rwork0.228 -
obs-10809
Solvent computationBsol: 52.222 Å2
Displacement parametersBiso mean: 13.3891 Å2
Baniso -1Baniso -2Baniso -3
1--0.089 Å20 Å20 Å2
2---0.089 Å20 Å2
3---0.178 Å2
Refinement stepCycle: LAST / Resolution: 1.77→24.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 56 148 1129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.299
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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