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- PDB-7pj3: Crystal structure of catalytic domain in open conformation of Lyt... -

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Basic information

Entry
Database: PDB / ID: 7pj3
TitleCrystal structure of catalytic domain in open conformation of LytB from Streptococcus pneumoniae
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 / TRIETHYLENE GLYCOL / Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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)31,5376
Polymers30,8961
Non-polymers6415
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint4 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.276, 92.614, 124.392
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 , 1 types, 1 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

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Non-polymers , 5 types, 186 molecules

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


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
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: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.43→46.31 Å / Num. obs: 50892 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.012 / Net I/σ(I): 31
Reflection shellResolution: 1.43→1.45 Å / Rmerge(I) obs: 0.775 / Num. unique obs: 2479 / Rpim(I) all: 0.219

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q2W

4q2w


Resolution: 1.43→43.434 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.225 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1852 2535 4.985 %
Rwork0.1438 48313 -
all0.146 --
obs-50848 99.994 %
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: 22.694 Å2
Baniso -1Baniso -2Baniso -3
1-2.288 Å2-0 Å20 Å2
2---1.56 Å20 Å2
3----0.729 Å2
Refinement stepCycle: LAST / Resolution: 1.43→43.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 41 181 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132355
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172152
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6373182
X-RAY DIFFRACTIONr_angle_other_deg1.7271.5884988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54524.153118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.141156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022702
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02542
X-RAY DIFFRACTIONr_nbd_refined0.2150.2422
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.21962
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21133
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1240.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.229
X-RAY DIFFRACTIONr_nbd_other0.2560.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1930.22
X-RAY DIFFRACTIONr_mcbond_it2.1632.0361136
X-RAY DIFFRACTIONr_mcbond_other2.0732.0341135
X-RAY DIFFRACTIONr_mcangle_it2.4923.0691434
X-RAY DIFFRACTIONr_mcangle_other2.4963.071435
X-RAY DIFFRACTIONr_scbond_it3.4212.521219
X-RAY DIFFRACTIONr_scbond_other3.422.5211220
X-RAY DIFFRACTIONr_scangle_it4.0273.6131748
X-RAY DIFFRACTIONr_scangle_other4.0263.6141749
X-RAY DIFFRACTIONr_lrange_it3.98724.5622659
X-RAY DIFFRACTIONr_lrange_other3.89724.2232628
X-RAY DIFFRACTIONr_rigid_bond_restr6.4534507
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
1.43-1.4670.2311710.16535420.16837140.9270.94699.97310.165
1.467-1.5070.2291800.15834280.16136080.9190.9421000.158
1.507-1.5510.1961730.13433460.13735190.9420.9591000.134
1.551-1.5990.1981870.12132450.12534320.9510.9631000.121
1.599-1.6510.1921500.11931790.12233290.9480.9661000.119
1.651-1.7090.1851360.11330680.11632040.9570.9711000.113
1.709-1.7730.1561570.10929470.11231040.9630.9741000.109
1.773-1.8450.1881730.12728420.1330150.950.9681000.127
1.845-1.9270.1651540.11727390.1228930.9680.9741000.117
1.927-2.0210.1761390.12125880.12427270.9560.9741000.121
2.021-2.130.1721070.12425000.12626070.9570.9721000.124
2.13-2.2590.1551270.12123830.12325100.9740.9771000.121
2.259-2.4150.1881180.12822090.13123270.9580.971000.128
2.415-2.6080.1861040.13421010.13722050.9620.9711000.134
2.608-2.8550.187900.14619180.14820080.9660.9711000.146
2.855-3.1910.1811040.15417400.15618440.9620.9661000.154
3.191-3.6810.18800.16315610.16416410.9580.9651000.163
3.681-4.50.162860.14113000.14213860.9720.9761000.141
4.5-6.330.22600.18210510.18411110.9690.9691000.182
6.33-43.4340.241390.2226270.2236660.9550.9511000.222

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