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- PDB-7pj4: Crystal structure of catalytic domain in closed conformation of L... -

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Basic information

Entry
Database: PDB / ID: 7pj4
TitleCrystal structure of catalytic domain in closed conformation of LytB (E585Q)from Streptococcus pneumoniae
ComponentsPutative endo-beta-N-acetylglucosaminidaseEndoglycosidase H
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 / Cell wall/choline-binding repeat / Cell wall-binding repeat profile.
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
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)31,4896
Polymers30,8951
Non-polymers5945
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint0 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.651, 92.679, 124.196
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 / Endoglycosidase H / Murein hydrolase


Mass: 30895.436 Da / Num. of mol.: 1 / Mutation: E585Q
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 , 6 types, 306 molecules

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


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


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 300 Bis-Tris buffer 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: 1.25→46.34 Å / Num. obs: 74735 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.02 / Net I/σ(I): 20.4
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 3690 / Rpim(I) all: 0.226

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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: 1.25→43.454 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.136 / SU B: 1.123 / SU ML: 0.023 / Average fsc free: 0.9681 / Average fsc work: 0.9749 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1623 3754 5.027 %
Rwork0.136 70929 -
all0.137 --
obs-74683 99.973 %
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: 14.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.953 Å2-0 Å20 Å2
2---0.439 Å20 Å2
3----0.515 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 38 301 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132387
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172195
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6383229
X-RAY DIFFRACTIONr_angle_other_deg1.7651.595092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22824.237118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82815408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.901156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022755
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02549
X-RAY DIFFRACTIONr_nbd_refined0.2220.2459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21957
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.160.21
X-RAY DIFFRACTIONr_metal_ion_refined0.150.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.217
X-RAY DIFFRACTIONr_nbd_other0.2150.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.150.22
X-RAY DIFFRACTIONr_mcbond_it1.21.2061156
X-RAY DIFFRACTIONr_mcbond_other1.1781.2051154
X-RAY DIFFRACTIONr_mcangle_it1.5121.8221463
X-RAY DIFFRACTIONr_mcangle_other1.5141.8231464
X-RAY DIFFRACTIONr_scbond_it2.4231.6111231
X-RAY DIFFRACTIONr_scbond_other2.4221.6111232
X-RAY DIFFRACTIONr_scangle_it2.8532.2741766
X-RAY DIFFRACTIONr_scangle_other2.8522.2741767
X-RAY DIFFRACTIONr_lrange_it3.00315.892775
X-RAY DIFFRACTIONr_lrange_other2.79815.1842707
X-RAY DIFFRACTIONr_rigid_bond_restr6.12434582
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
1.25-1.2820.2533030.21351640.21654670.9390.9521000.213
1.282-1.3180.1932720.1650590.16253310.9650.9711000.16
1.318-1.3560.192500.14249280.14451780.9620.9711000.142
1.356-1.3970.1652610.12247840.12450450.9680.9761000.122
1.397-1.4430.1582600.10746280.1148890.9730.9899.97950.107
1.443-1.4940.1482260.1145090.11247350.9720.9771000.11
1.494-1.550.1612390.10943170.11245560.9670.9781000.109
1.55-1.6130.1452210.10641830.10844040.9750.9821000.106
1.613-1.6850.1482100.10440230.10642340.9750.98399.97640.104
1.685-1.7670.1581980.11438210.11640190.9690.9781000.114
1.767-1.8620.1571730.11837170.1238900.9720.9781000.118
1.862-1.9750.1551680.12534470.12636150.970.9791000.125
1.975-2.1110.1471860.12432640.12534500.9780.981000.124
2.111-2.280.1371470.12330670.12432160.980.98199.93780.123
2.28-2.4970.1271320.11828230.11829640.9820.98399.69640.118
2.497-2.790.1491490.14525470.14526960.9750.9741000.145
2.79-3.220.1811180.15222800.15423990.9630.96499.95830.152
3.22-3.9380.169990.14719430.14820450.9670.96999.85330.147
3.938-5.5470.167920.16115160.16116090.9710.97699.93790.161
5.547-43.4540.231500.229090.229590.9550.961000.22

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