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- PDB-5leo: Complex structure of lysostaphin SH3b domain with peptidoglycan f... -

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Basic information

Entry
Database: PDB / ID: 5leo
TitleComplex structure of lysostaphin SH3b domain with peptidoglycan fragment
Components
  • GLY-GLY-GLY-GLY-GLY
  • Lysostaphin
KeywordsCELL ADHESION / lysostaphin / peptidoglycan / complex / cell wall targeting/binding domain / SH3
Function / homology
Function and homology information


lysostaphin / cell wall organization / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Lysostaphin, N-terminal domain / Domain of unknown function (DUF6721) / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / SH3 Domains ...Lysostaphin, N-terminal domain / Domain of unknown function (DUF6721) / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / SH3 Domains / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcaceae (Staphylococcus group)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJagielska, E. / Nowak, E. / Bochtler, M. / Sabala, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
The National Center for Research and DevelopmentPBS1/A8/8/2012 Poland
CitationJournal: To Be Published
Title: Complex structure of lysostaphin SH3doamin with peptidoglycan fragment
Authors: Jagielska, E. / Nowak, E. / Bochtler, M. / Sabala, I.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
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

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Assembly

Deposited unit
A: Lysostaphin
B: Lysostaphin
G: GLY-GLY-GLY-GLY-GLY
H: GLY-GLY-GLY-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,56112
Polymers21,7484
Non-polymers8138
Water4,774265
1
A: Lysostaphin
H: GLY-GLY-GLY-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1855
Polymers10,8742
Non-polymers3103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysostaphin
G: GLY-GLY-GLY-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3777
Polymers10,8742
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.380, 54.364, 63.229
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 Lysostaphin / / Glycyl-glycine endopeptidase


Mass: 10570.948 Da / Num. of mol.: 2 / Fragment: SH3b domain, UNP Residues 401-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcaceae (Staphylococcus group)
Gene: lss / Production host: Escherichia coli (E. coli) / References: UniProt: P10547, lysostaphin
#2: Protein/peptide GLY-GLY-GLY-GLY-GLY


Mass: 303.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcaceae (Staphylococcus group)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Buffer system 3 (0.1 M Tris (base), Bicine buffer, pH 8.5), 0.09 M NPS (NaNO3, Na2HPO4, (NH4)SO4), 37.5% MPD (racemic), PEG 1000, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.57→60 Å / Num. obs: 25084 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 5.25

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXC

4lxc


Resolution: 1.6→39.402 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.2351 1198 5.11 %
Rwork0.184 --
obs0.1866 23461 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 46 265 1827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071605
X-RAY DIFFRACTIONf_angle_d1.1152184
X-RAY DIFFRACTIONf_dihedral_angle_d14.796560
X-RAY DIFFRACTIONf_chiral_restr0.048228
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.66410.32041210.27682443X-RAY DIFFRACTION100
1.6641-1.73980.32031220.25372460X-RAY DIFFRACTION100
1.7398-1.83150.26741170.22572430X-RAY DIFFRACTION100
1.8315-1.94630.27651430.22452438X-RAY DIFFRACTION99
1.9463-2.09660.25371320.1912443X-RAY DIFFRACTION100
2.0966-2.30750.22221370.16952469X-RAY DIFFRACTION100
2.3075-2.64140.22261550.17182462X-RAY DIFFRACTION100
2.6414-3.32760.2091340.16042502X-RAY DIFFRACTION100
3.3276-39.41380.19761370.15012616X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -27.8405 Å / Origin y: 4.0045 Å / Origin z: 82.5817 Å
111213212223313233
T0.0966 Å20.0023 Å20.0097 Å2-0.0773 Å20.006 Å2--0.0772 Å2
L1.0983 °2-0.0841 °20.1698 °2-0.2436 °20.1456 °2--0.1368 °2
S0.003 Å °-0.0218 Å °-0.0078 Å °-0.0078 Å °0.0025 Å °-0.006 Å °0.0034 Å °-0.0055 Å °-0.0059 Å °
Refinement TLS groupSelection details: all

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