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- PDB-2wwd: 3D-structure of the modular autolysin LytC from Streptococcus pne... -

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Basic information

Entry
Database: PDB / ID: 2wwd
Title3D-structure of the modular autolysin LytC from Streptococcus pneumoniae in complex with pneummococcal peptidoglycan fragment
Components1,4-BETA-N-ACETYLMURAMIDASE
KeywordsHYDROLASE / GLYCOSIDASE / CHOLINE-BINDING PROTEINS
Function / homology
Function and homology information


peptidoglycan beta-N-acetylmuramidase / peptidoglycan beta-N-acetylmuramidase activity / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity
Similarity search - Function
Choline-binding repeat / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Choline-binding repeat / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ALANINE / CHOLINE ION / GLUTAMINE / 1,4-beta-N-acetylmuramidase / 1,4-beta-N-acetylmuramidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPerez-Dorado, I. / Sanles, R. / Hermoso, J.A. / Gonzalez, A. / Garcia, A. / Garcia, P. / Garcia, J.L.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Insights Into Pneumococcal Fratricide from the Crystal Structures of the Modular Killing Factor Lytc.
Authors: Perez-Dorado, I. / Gonzalez, A. / Morales, M. / Sanles, R. / Striker, W. / Vollmer, W. / Mobashery, S. / Garcia, J.L. / Martinez-Ripoll, M. / Garcia, P. / Hermoso, J.A.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Insights Into the Structure-Function Relationships of Pneumococcal Cell Wall Lysozymes, Lytc and Cpl- 1.
Authors: Monterroso, B. / Saiz, J.L. / Garcia, P. / Garcia, J.L. / Menendez, M.
#2: Journal: Biochem.J. / Year: 2005
Title: Unravelling the Structure of the Pneumococcal Autolytic Lysozyme.
Authors: Monterroso, B. / Lopez-Zumel, C. / Garcia, J.L. / Saiz, J.L. / Garcia, P. / Campillo, N.E. / Menendez, M.
#3: Journal: Mol.Microbiol. / Year: 1999
Title: The Molecular Characterization of the First Autolytic Lysozyme of Streptococcus Pneumoniae Reveals Evolutionary Mobile Domains.
Authors: Garcia, P. / Paz Gonzalez, M. / Garcia, E. / Garcia, J.L. / Lopez, R.
History
DepositionOct 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2013Group: Database references / Derived calculations / Non-polymer description
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 / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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.occupancy / _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_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.pdbx_num_residues
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _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 3.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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: 1,4-BETA-N-ACETYLMURAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37618
Polymers55,2711
Non-polymers2,10617
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 66.870, 77.920
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein 1,4-BETA-N-ACETYLMURAMIDASE / LYTC AUTOLYSIN


Mass: 55270.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PLCC14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z4J8, UniProt: Q8DP07*PLUS, 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 , 5 types, 152 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H14NO
#5: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


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


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsENTRY ACCESSION CODE CORRESPONDS TO THE IMMATURE PROTEIN WHICH POSSESSES A SIGNAL PEPTIDE OF 33 ...ENTRY ACCESSION CODE CORRESPONDS TO THE IMMATURE PROTEIN WHICH POSSESSES A SIGNAL PEPTIDE OF 33 AMINO-ACIDS BUT THE STRUCTURE HERE REPORTED CORRESPONDS TO THE MATURE FORM. THE FIRST AMINO-ACID OF THE MATURE PROTEIN IS REFERED AS TO RESIDUE 1.

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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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→75 Å / Num. obs: 27909 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WW5

2ww5


Resolution: 2.25→57.17 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.134 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FIRST 37 AA OF THE POLYPEPTIDE CHAIN WERE NOT MODELLED DUE TO POOR ELECTRON DENSITY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1925 6.9 %RANDOM
Rwork0.204 ---
obs0.206 25982 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.73 Å2
2---0.42 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.25→57.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 138 136 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9365273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20524.434212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44415614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6121513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023025
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22589
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.52181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98123395
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15832098
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8024.51878
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 152 -
Rwork0.275 1897 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4282-1.2355-0.73354.07160.18583.7297-0.06630.1623-0.03040.31720.1602-0.01950.25910.1184-0.09380.0382-0.0273-0.0006-0.0326-0.0479-0.084831.3182-53.40083.546
20.26190.64120.14852.36620.91950.4722-0.0588-0.03310.0435-0.12010.070.06090.01820.0197-0.01120.0209-0.0344-0.032-0.0374-0.002-0.017531.5136-16.270318.3963
35.9565-5.6482-5.278611.42828.595110.3428-0.0234-0.00590.3414-0.1347-0.66680.9701-0.1516-0.08610.6903-0.1437-0.0589-0.035-0.0625-0.16240.230433.712421.703528.5084
47.49750.497-1.452.7944-0.01553.15450.5791-0.35260.81010.2118-0.2556-0.0134-0.44550.2864-0.3234-0.0329-0.06320.1402-0.1221-0.03320.141414.84131.112933.0489
51.86150.37840.26930.44880.17320.83650.02540.1954-0.1032-0.02440.0215-0.05930.0023-0.0229-0.0469-0.03410.00590.0262-0.0207-0.0032-0.02451.939914.506122.6326
61.7998-0.4356-2.60280.23581.1716.010.16790.5722-0.8409-0.40090.2757-0.31350.41920.6253-0.44360.01980.0599-0.07750.0465-0.15250.03089.01331.90028.714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 76
2X-RAY DIFFRACTION2A77 - 217
3X-RAY DIFFRACTION3A218 - 242
4X-RAY DIFFRACTION4A243 - 267
5X-RAY DIFFRACTION5A268 - 365
6X-RAY DIFFRACTION5A381 - 468
7X-RAY DIFFRACTION6A366 - 380

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