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- PDB-7pl2: Crystal structure of choline-binding module of LytB from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 7pl2
TitleCrystal structure of choline-binding module 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 / Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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 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 / 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
A: Putative endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,29918
Polymers48,5281
Non-polymers1,77117
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint87 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.100, 202.100, 26.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

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


Mass: 48528.203 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: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979312 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979312 Å / Relative weight: 1
ReflectionResolution: 2.98→48.54 Å / Num. obs: 12892 / % possible obs: 97.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.117 / Net I/σ(I): 4.2
Reflection shellResolution: 2.98→3.16 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2036 / Rpim(I) all: 0.467

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CNL

4cnl


Resolution: 2.98→43.76 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 643 5 %
Rwork0.2187 12227 -
obs0.2215 12870 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.18 Å2 / Biso mean: 67.683 Å2 / Biso min: 28.34 Å2
Refinement stepCycle: final / Resolution: 2.98→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 357 26 3791
Biso mean--58.12 48.49 -
Num. residues----398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.210.34990.31192415251497
3.21-3.530.30091240.27882376250096
3.53-4.040.31821300.21552465259598
4.04-5.090.24121600.1782440260096
5.09-43.760.25261300.20732531266194
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)
14.2172.55431.92692.34560.8912.83360.30020.6347-0.5222-0.19740.09680.00850.1789-0.0302-0.17530.30040.0250.03830.6315-0.0020.3329-117.101796.6418-25.7531
22.9292-1.37191.62481.0137-0.1960.82120.40270.2569-0.7659-0.0837-0.03960.25050.15580.1486-0.28060.42210.0532-0.08220.660.00960.6699-87.359386.7582-8.6933
31.6789-1.1144-0.07073.7784-0.10042.61080.0242-0.22620.24510.0489-0.0050.1316-0.0472-0.06490.00520.2958-0.0668-0.03260.33280.02850.1088-52.820977.3735.8169
41.44390.83031.53141.39540.58140.75030.60460.8345-1.30410.55640.1269-0.96930.89490.74-0.3140.4570.1204-0.20330.6457-0.150.8647-30.674866.705813.7836
50.36740.01360.03682.59962.70453.2210.33050.0143-0.53280.05140.2564-0.35440.18820.4055-0.77240.49580.0586-0.12550.9789-0.05190.6126-15.538970.343817.3022
61.0803-0.4317-0.69521.26570.01771.36140.72441.3509-0.5298-0.869-0.19590.90620.65410.38670.04160.78160.1193-0.35260.9492-0.25470.9584-8.234360.799415.6479
72.4219-2.6292-2.88877.85714.22056.45850.56040.0538-1.70050.6569-0.42290.4230.98930.0889-0.14650.57060.043-0.14040.6375-0.00150.9178-2.142157.354126.4253
82.40420.2879-3.01580.9034-1.41815.68830.31780.2765-0.13260.0427-0.22750.1618-0.23980.73590.15420.61560.0415-0.07210.8177-0.130.55088.778962.690625.5525
94.15722.5886-0.58123.69670.91170.8505-0.16490.0736-1.0308-0.0159-0.0862-1.15480.20230.57970.50890.74730.2119-0.13611.0779-0.12541.003915.557853.753925.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 76 )A2 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 163 )A77 - 163
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 242 )A164 - 242
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 286 )A243 - 286
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 307 )A287 - 307
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 330 )A308 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 351 )A331 - 351
8X-RAY DIFFRACTION8chain 'A' and (resid 352 through 374 )A352 - 374
9X-RAY DIFFRACTION9chain 'A' and (resid 375 through 399 )A375 - 399

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