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- PDB-7pj5: Crystal structure of catalytic domain of LytB from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 7pj5
TitleCrystal structure of catalytic domain of LytB from Streptococcus pneumoniae in complex with NAG-NAG-NAG-NAG tetrasaccharide
ComponentsPutative endo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / glucosaminidase / peptidoglycan hydrolase
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / amidase activity / cell wall organization / extracellular region
Similarity search - Function
Peptidoglycan hydrolase LytB, WW-like domain / Endo-beta-N-acetylglucosaminidase LytB, WW domain / Peptidoglycan hydrolase LytB WW-like domain / Endo-beta-N-acetylglucosaminidase LytB SH3 domain / Choline-binding repeat / : / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Putative cell wall binding repeat ...Peptidoglycan hydrolase LytB, WW-like domain / Endo-beta-N-acetylglucosaminidase LytB, WW domain / Peptidoglycan hydrolase LytB WW-like domain / Endo-beta-N-acetylglucosaminidase LytB SH3 domain / Choline-binding repeat / : / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
CitationJournal: Cell Rep / Year: 2023
Title: Molecular basis of the final step of cell division in Streptococcus pneumoniae.
Authors: Martinez-Caballero, S. / Freton, C. / Molina, R. / Bartual, S.G. / Gueguen-Chaignon, V. / Mercy, C. / Gago, F. / Mahasenan, K.V. / Munoz, I.G. / Lee, M. / Hesek, D. / Mobashery, S. / ...Authors: Martinez-Caballero, S. / Freton, C. / Molina, R. / Bartual, S.G. / Gueguen-Chaignon, V. / Mercy, C. / Gago, F. / Mahasenan, K.V. / Munoz, I.G. / Lee, M. / Hesek, D. / Mobashery, S. / Hermoso, J.A. / Grangeasse, C.
History
DepositionAug 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Putative endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2186
Polymers30,8961
Non-polymers1,3215
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint22 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.679, 92.358, 124.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein Putative endo-beta-N-acetylglucosaminidase / Murein hydrolase


Mass: 30896.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: lytB, spr0867 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P59206, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 179 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 300 Bis-Tris Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.55→46.18 Å / Num. obs: 40276 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Net I/σ(I): 24.5
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.701 / Num. unique obs: 1981 / Rpim(I) all: 0.199

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PJ3

7pj3


Resolution: 1.55→46.174 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.807 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1917 1991 4.948 %
Rwork0.1436 38244 -
all0.146 --
obs-40235 99.975 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.171 Å2-0 Å20 Å2
2---1.672 Å20 Å2
3---0.501 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 88 175 2437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132362
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172149
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6743196
X-RAY DIFFRACTIONr_angle_other_deg1.9311.624986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09424.224116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75315386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.472156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02536
X-RAY DIFFRACTIONr_nbd_refined0.2080.2430
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21870
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21140
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2580.222
X-RAY DIFFRACTIONr_nbd_other0.3230.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2290.21
X-RAY DIFFRACTIONr_mcbond_it2.7692.1481116
X-RAY DIFFRACTIONr_mcbond_other2.7412.1461115
X-RAY DIFFRACTIONr_mcangle_it3.13.2361402
X-RAY DIFFRACTIONr_mcangle_other3.1033.2371403
X-RAY DIFFRACTIONr_scbond_it3.6612.6191246
X-RAY DIFFRACTIONr_scbond_other3.662.6191247
X-RAY DIFFRACTIONr_scangle_it4.1843.771794
X-RAY DIFFRACTIONr_scangle_other4.1833.771795
X-RAY DIFFRACTIONr_lrange_it4.1726.0652646
X-RAY DIFFRACTIONr_lrange_other4.10225.7482616
X-RAY DIFFRACTIONr_rigid_bond_restr5.72434511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.2071550.12127860.12629410.9430.961000.121
1.59-1.6340.2571290.13627330.14128620.9120.9491000.136
1.634-1.6810.2171570.12626190.13127760.9390.961000.126
1.681-1.7330.2141240.12125910.12527150.9430.9631000.121
1.733-1.790.2041380.11224720.11626110.9440.96899.96170.112
1.79-1.8520.2131330.11124280.11625610.9470.9711000.111
1.852-1.9220.1571230.10623360.10824590.9690.9751000.106
1.922-20.1791030.11522630.11823660.9630.9741000.115
2-2.0890.1771120.11821580.12122700.9630.9741000.118
2.089-2.1910.1511010.1120690.11221700.9710.9791000.11
2.191-2.3090.1621100.11819630.12120730.9690.9761000.118
2.309-2.4490.186910.12918860.13219790.9640.97299.89890.129
2.449-2.6170.176890.14717580.14918470.9570.9641000.147
2.617-2.8260.208850.15616580.15817430.9480.9641000.156
2.826-3.0950.19850.1615080.16115940.9520.96299.93730.16
3.095-3.4580.209790.16213900.16414700.9410.96499.9320.162
3.458-3.9890.165550.15412370.15512930.9720.97199.92270.154
3.989-4.8770.175450.14110540.14211000.9760.97699.90910.141
4.877-6.8590.226570.1968230.1988810.9510.95599.88650.196
6.859-46.1740.269200.2075120.2095320.9330.9561000.207

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