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- PDB-5ctv: Catalytic domain of LytA, the major autolysin of Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 5ctv
TitleCatalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment
Components
  • Autolysin
  • fragment of peptidoglycan
KeywordsHYDROLASE / LytA / pneumococci / autolysis / amidase / peptidoglycan complex / antibiotics
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
Streptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsAchour, A. / Sandalova, T. / Mellroth, P.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity.
Authors: Sandalova, T. / Lee, M. / Henriques-Normark, B. / Hesek, D. / Mobashery, S. / Mellroth, P. / Achour, A.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autolysin
C: fragment of peptidoglycan
E: fragment of peptidoglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1814
Polymers22,1783
Non-polymers1,0031
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint13 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.566, 54.623, 78.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Autolysin / Cell wall hydrolase / Mucopeptide aminohydrolase / Murein hydrolase / N-acetylmuramoyl-L-alanine amidase


Mass: 21199.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-180 / Mutation: C60A, H133A, C136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: lytA, SP_1937
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Protein/peptide fragment of peptidoglycan


Mass: 489.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae (bacteria)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 1002.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: PEG 6000, 1M LiCl, 0.1M Tris HCl / PH range: 5.9-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.05→45 Å / Num. obs: 90326 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 65.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IVV

4ivv


Resolution: 1.05→44.91 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.728 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15273 4525 5 %RANDOM
Rwork0.13383 ---
obs0.13477 85673 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20 Å2
2--0.11 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.05→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 248 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191568
X-RAY DIFFRACTIONr_bond_other_d0.0010.021423
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9772130
X-RAY DIFFRACTIONr_angle_other_deg0.82633272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80224.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.56715233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.948157
X-RAY DIFFRACTIONr_chiral_restr0.2410.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8650.718739
X-RAY DIFFRACTIONr_mcbond_other0.7570.713738
X-RAY DIFFRACTIONr_mcangle_it1.0571.07921
X-RAY DIFFRACTIONr_mcangle_other1.0771.075922
X-RAY DIFFRACTIONr_scbond_it1.1870.869829
X-RAY DIFFRACTIONr_scbond_other1.2020.869829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5861.2551203
X-RAY DIFFRACTIONr_long_range_B_refined2.3347.521998
X-RAY DIFFRACTIONr_long_range_B_other1.7056.6081857
X-RAY DIFFRACTIONr_rigid_bond_restr1.51432989
X-RAY DIFFRACTIONr_sphericity_free28.649565
X-RAY DIFFRACTIONr_sphericity_bonded6.28453126
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 345 -
Rwork0.222 6223 -
obs--99.27 %

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