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- PDB-7pl5: Crystal structure of choline-binding module (R1-R9) of LytB from ... -

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Basic information

Entry
Database: PDB / ID: 7pl5
TitleCrystal structure of choline-binding module (R1-R9) of LytB from Streptococcus pneumoniae
ComponentsPutative endo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / glucosaminidase / peptidoglycan hydrolase / choline-binding
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
CHOLINE ION / TRIETHYLENE GLYCOL / Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMolina, R. / Martinez 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 28, 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 / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
BBB: Putative endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,17719
Polymers43,5152
Non-polymers1,66217
Water3,819212
1
AAA: Putative endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5149
Polymers21,7581
Non-polymers7568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Putative endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,66410
Polymers21,7581
Non-polymers9069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.299, 96.143, 49.096
Angle α, β, γ (deg.)90.000, 100.966, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 1 - 177 / Label seq-ID: 1 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 21757.713 Da / Num. of mol.: 2
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: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: MES buffer Zinc sulfate PEG 6000

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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: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.99→48.2 Å / Num. obs: 28181 / % possible obs: 98.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.238 / Rpim(I) all: 0.108 / Net I/σ(I): 6
Reflection shellResolution: 1.99→2.03 Å / Rmerge(I) obs: 0.952 / Num. unique obs: 1665 / Rpim(I) all: 0.496

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V05

2v05


Resolution: 1.99→44.504 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.885 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.176 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2328 1439 5.115 %
Rwork0.1723 26695 -
all0.175 --
obs-28134 99.245 %
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: 25.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.866 Å2-0 Å21.014 Å2
2---0.332 Å20 Å2
3----0.862 Å2
Refinement stepCycle: LAST / Resolution: 1.99→44.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 98 212 3339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123230
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182871
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6314371
X-RAY DIFFRACTIONr_angle_other_deg1.5121.5966565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76924.944180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07415493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.099152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_nbd_refined0.2070.2528
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22684
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21523
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2208
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.238
X-RAY DIFFRACTIONr_nbd_other0.2930.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1210.21
X-RAY DIFFRACTIONr_mcbond_it2.9832.2591452
X-RAY DIFFRACTIONr_mcbond_other2.9742.2561451
X-RAY DIFFRACTIONr_mcangle_it4.2023.3691815
X-RAY DIFFRACTIONr_mcangle_other4.2023.3721816
X-RAY DIFFRACTIONr_scbond_it3.982.8461778
X-RAY DIFFRACTIONr_scbond_other3.9792.8481779
X-RAY DIFFRACTIONr_scangle_it5.9984.0592556
X-RAY DIFFRACTIONr_scangle_other5.9964.0612557
X-RAY DIFFRACTIONr_lrange_it7.70425.733852
X-RAY DIFFRACTIONr_lrange_other7.725.6453827
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.055795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.10820.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.10820.05009
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
1.99-2.0420.2371100.21418210.21521000.9080.90591.95240.214
2.042-2.0970.261910.18819240.19120150.910.9261000.188
2.097-2.1580.213900.1819120.18120070.9240.93499.75090.18
2.158-2.2240.265910.19118170.19519080.9130.931000.191
2.224-2.2970.26970.18617430.19118410.9090.92799.94570.186
2.297-2.3770.234880.17517140.17818030.9140.93399.94450.175
2.377-2.4670.219880.1616540.16317450.930.94699.82810.16
2.467-2.5670.25820.16615930.17116760.9240.94599.94030.166
2.567-2.6810.244750.15615250.1616000.9220.9521000.156
2.681-2.8110.249800.15814640.16215450.9240.95599.93530.158
2.811-2.9630.213690.15213720.15514450.9340.95599.72320.152
2.963-3.1420.214740.1613190.16313960.9310.95299.78510.16
3.142-3.3570.229940.16311950.16812920.9430.9599.76780.163
3.357-3.6250.23700.17411410.17712130.9340.94299.83510.174
3.625-3.9680.255600.16410660.16911280.9350.95399.82270.164
3.968-4.4320.163480.1459560.14610080.9620.96799.60320.145
4.432-5.1090.225400.1698580.1729010.9460.96699.6670.169
5.109-6.2370.251420.2257270.2267710.9570.95199.74060.225
6.237-8.7350.233360.195600.1935960.9250.9491000.19
8.735-44.5040.307140.2283340.2323490.8710.91599.71350.228

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