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- PDB-5i8l: Crystal structure of the full-length cell wall-binding module of ... -

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Basic information

Entry
Database: PDB / ID: 5i8l
TitleCrystal structure of the full-length cell wall-binding module of Cpl7 mutant R223A
ComponentsLysozyme
KeywordsHYDROLASE / cell-wall binding domain
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Cpl-7 lysozyme, C-terminal / CW_7 repeat / Cpl-7 lysozyme C-terminal domain / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesStreptococcus phage Cp-7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsBernardo-Garcia, N. / Silva-Martin, N. / Uson, I. / Hermoso, J.A.
CitationJournal: Sci Rep / Year: 2017
Title: Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan.
Authors: Bustamante, N. / Iglesias-Bexiga, M. / Bernardo-Garcia, N. / Silva-Martin, N. / Garcia, G. / Campanero-Rhodes, M.A. / Garcia, E. / Uson, I. / Buey, R.M. / Garcia, P. / Hermoso, J.A. / Bruix, M. / Menendez, M.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7102
Polymers15,6181
Non-polymers921
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.524, 50.331, 86.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme / / CP-7 lysin / Endolysin / Muramidase


Mass: 15617.854 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage Cp-7 (virus) / Gene: CPL7 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P19385, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.1 M tri-Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.05793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05793 Å / Relative weight: 1
ReflectionResolution: 2.8→43.04 Å / Num. obs: 2800 / % possible obs: 81.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cvd

4cvd


Resolution: 2.801→14.873 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.92
RfactorNum. reflection% reflection
Rfree0.2891 84 3.05 %
Rwork0.2062 --
obs0.2088 2758 80.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→14.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 6 6 1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051104
X-RAY DIFFRACTIONf_angle_d1.2691507
X-RAY DIFFRACTIONf_dihedral_angle_d19.297392
X-RAY DIFFRACTIONf_chiral_restr0.048171
X-RAY DIFFRACTIONf_plane_restr0.004206
LS refinement shellResolution: 2.6→2.8 Å
RfactorNum. reflection% reflection
Rfree0.3567 84 -
Rwork0.3289 2674 -
obs--80 %
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)
12.8166-0.42090.7453.50230.23572.40970.1628-0.1749-0.09390.4170.10350.1301-0.34110.1595-0.02220.2214-0.05060.04790.1521-0.06530.0072-10.468940.551212.0186
22.3489-0.6621.17925.271-3.81692.9783-0.3154-0.1681-0.06780.03650.0475-0.11910.41180.84280.28190.13830.1137-0.05920.24830.01440.175-5.786440.41411.71
31.32770.63-1.05193.1948-0.18591.2256-0.3881-0.1434-0.1224-0.07250.110.58840.054-0.41730.0268-0.06820.0534-0.04280.13440.03570.2622-4.445854.6546-0.4692
42.53561.1588-1.27241.81351.55454.19430.2928-0.2737-0.0050.20210.1345-0.33960.58160.4817-0.14940.1901-0.0334-0.00270.21480.020.08122.929747.9347-2.145
52.4897-1.9527-2.28984.50254.16333.9897-0.0439-0.41620.0360.2274-0.09120.1039-0.0082-0.1861-0.13810.11660.01380.07040.25550.00940.19985.04460.46191.6136
61.10351.38551.16532.979-0.79835.3471-0.29-0.0791-0.1430.1175-0.19250.12320.2083-0.5520.26440.10250.01680.05230.10580.06680.25137.107555.525813.2187
72.1371-0.30051.14483.1454-1.41632.66810.0159-0.4749-0.13350.52060.34980.315-0.1251-0.71380.02010.28250.0081-0.02780.17530.09790.01814.713862.467511.8996
84.0476-2.62380.39623.11410.35532.7421-0.09680.0117-0.76050.3465-0.2198-0.15070.11430.08280.11610.10530.0938-0.09520.40750.07240.392314.250751.804620.5376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 199 through 233 )
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 247 )
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 262 )
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 295 )
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 316 )
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 329 )
8X-RAY DIFFRACTION8chain 'A' and (resid 330 through 341 )

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