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- PDB-4q2w: Crystal Structure of pneumococcal peptidoglycan hydrolase LytB -

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Basic information

Entry
Database: PDB / ID: 4q2w
TitleCrystal Structure of pneumococcal peptidoglycan hydrolase LytB
ComponentsPutative endo-beta-N-acetylglucosaminidaseEndoglycosidase H
KeywordsHYDROLASE / all-beta module / GH73
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
Putative endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsBai, X.H. / Chen, H.J. / Jiang, Y.L. / Wen, Z. / Cheng, W. / Li, Q. / Zhang, J.R. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of pneumococcal peptidoglycan hydrolase LytB reveals insights into the bacterial cell wall remodeling and pathogenesis.
Authors: Bai, X.H. / Chen, H.J. / Jiang, Y.L. / Wen, Z. / Huang, Y. / Cheng, W. / Li, Q. / Qi, L. / Zhang, J.R. / Chen, Y. / Zhou, C.Z.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)33,4455
Polymers33,0771
Non-polymers3684
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.828, 44.593, 52.221
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33077.027 Da / Num. of mol.: 1 / Fragment: UNP residues 375-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: lytB, SP_0965 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/B834(DE3)
References: UniProt: P59205, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 43.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6
Details: 15% PEG 6000, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 34504 / Num. obs: 33952 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 14.855
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.167 / Num. unique all: 3070 / Rsym value: 0.656 / % possible all: 89.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→33.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.426 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21726 1626 5 %RANDOM
Rwork0.18058 ---
all0.18058 32768 --
obs0.18252 30697 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 24 171 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192162
X-RAY DIFFRACTIONr_bond_other_d0.0010.021999
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9592910
X-RAY DIFFRACTIONr_angle_other_deg0.72234614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66425.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.66156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_mcbond_it1.8813.5151050
X-RAY DIFFRACTIONr_mcbond_other1.8753.5141049
X-RAY DIFFRACTIONr_mcangle_it2.875.261309
X-RAY DIFFRACTIONr_mcangle_other2.8715.2611310
X-RAY DIFFRACTIONr_scbond_it2.4513.8871112
X-RAY DIFFRACTIONr_scbond_other2.4513.8871112
X-RAY DIFFRACTIONr_scangle_other3.9995.6841602
X-RAY DIFFRACTIONr_long_range_B_refined6.41229.4892603
X-RAY DIFFRACTIONr_long_range_B_other6.22129.1092544
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 89 -
Rwork0.338 1707 -
obs--71.02 %

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