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- PDB-2ixu: Crystal structure of the modular Cpl-1 endolysin complexed with a... -

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Entry
Database: PDB / ID: 2ixu
TitleCrystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin)
ComponentsLYSOZYME
KeywordsHYDROLASE / ANTIMICROBIAL / MUEIN HYDROLASE / BACTERIOLYTIC ENZYME / PNEUMOCOCCAL CELL WALL DEGRADATION / LYSOZYME / GLYCOSIDASE / MULTIMODULAR
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to bacterium
Similarity search - Function
Multimodular pneumococcal cell wall endolysin, domain 3 / Multimodular pneumococcal cell wall endolysin, domain 3 / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Cholin Binding ...Multimodular pneumococcal cell wall endolysin, domain 3 / Multimodular pneumococcal cell wall endolysin, domain 3 / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Single Sheet / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ALANINE / FORMIC ACID / D-alpha-glutamine / Lysozyme
Similarity search - Component
Biological speciesSTREPTOCOCCUS PHAGE CP-1 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPerez-Dorado, I. / Hermoso, J.A.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Elucidation of the Molecular Recognition of Bacterial Cell Wall by Modular Pneumococcal Phage Endolysin Cpl-1.
Authors: Perez-Dorado, I. / Campillo, N.E. / Monterroso, B. / Hesek, D. / Lee, M. / Paez, J.A. / Garcia, P. / Martinez-Ripoll, M. / Garcia, J.L. / Mobashery, S. / Menendez, M. / Hermoso, J.A.
#1: Journal: Structure (London) / Year: 2003
Title: Structural Basis for Selective Recognition of Pneumococcal Cell Wall by Modular Endolysin from Phage Cp-1
Authors: Hermoso, J.A. / Monterroso, B. / Albert, A. / Galan, B. / Ahrazem, O. / Garcia, P. / Martinez-Ripoll, M. / Garcia, J.L. / Menendez, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Complete Modular Endolysin from Cp-1, a Phage Infecting Streptococcus Pneumoniae
Authors: Monterroso, B. / Albert, A. / Martinez-Ripoll, M. / Garcia, P. / Garcia, J.L. / Menendez, M. / Hermoso, J.A.
History
DepositionJul 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Apr 10, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site.pdbx_num_residues
Revision 3.0Jul 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 4.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 4.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)39,9995
Polymers39,2211
Non-polymers7784
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.521, 96.504, 127.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein LYSOZYME / ENDOLYSIN / MURAMIDASE / CP-1 LYSIN / CPL-1


Mass: 39221.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PHAGE CP-1 (virus) / Production host: ESCHERICHIA COLI DH1 (bacteria) / References: UniProt: P15057, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 175 molecules

#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical ChemComp-ZGL / D-alpha-glutamine / Iso-D-glutamine


Type: D-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.17 Å3/Da / Density % sol: 61.21 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 14, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→25.86 Å / Num. obs: 32678 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.6
Reflection shellResolution: 2.26→2.41 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H09

1h09


Resolution: 2.28→25.32 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26238 1573 6.9 %RANDOM
Rwork0.21236 ---
obs0.21236 21331 99.71 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.773 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---1.56 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.28→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 51 172 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.566
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1451.5
X-RAY DIFFRACTIONc_mcangle_it2.1012
X-RAY DIFFRACTIONc_scbond_it2.6673
X-RAY DIFFRACTIONc_scangle_it3.9564.5
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.399 107
Rwork0.305 1510

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