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- PDB-7bng: Complex structure of SH3b domain with L-canavanine -

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Basic information

Entry
Database: PDB / ID: 7bng
TitleComplex structure of SH3b domain with L-canavanine
ComponentsLysostaphin
KeywordsCELL ADHESION / CELL WALL TARGETING/BINDING / CWT / SH3 / COMPLEX / L-canavanine / Staphylococcus simulans
Function / homology
Function and homology information


lysostaphin / metallopeptidase activity
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
L-CANAVANINE / lysostaphin
Similarity search - Component
Biological speciesStaphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsMalecki, P.H. / Sabala, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-3D8D/16-00 Poland
CitationJournal: To Be Published
Title: Complex structure of SH3b domain with L-canavanine
Authors: Malecki, P.H. / Sabala, I.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysostaphin
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,47910
Polymers21,6382
Non-polymers8418
Water4,053225
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5648
Polymers10,8191
Non-polymers7457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9152
Polymers10,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.898, 55.232, 48.994
Angle α, β, γ (deg.)90.000, 93.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysostaphin


Mass: 10819.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus simulans (bacteria) / Gene: HMPREF3215_01322 / Production host: Escherichia coli (E. coli) / Strain (production host): magic / References: UniProt: A0A133QQ41, lysostaphin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% PEG 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.47→36.833 Å / Num. obs: 33240 / % possible obs: 98.7 % / Redundancy: 6.732 % / Biso Wilson estimate: 22.417 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Χ2: 0.806 / Net I/σ(I): 14.9 / Num. measured all: 223756
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.566.7361.1841.5935555540852780.7691.28297.6
1.56-1.666.8050.7692.534244510150320.8020.83298.6
1.66-1.86.0560.4474.0228166475246510.9070.48997.9
1.8-1.977.0370.2557.7130683436443600.9740.27599.9
1.97-2.27.0180.13413.9627673395039430.9920.14599.8
2.2-2.546.8930.09519.8323980349834790.9950.10399.5
2.54-3.116.510.05829.3718976296729150.9980.06398.2
3.11-4.386.6910.02656.77151282309226110.02897.9
4.38-36.8337.0790.02663.5393511322132110.02899.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LEO

5leo


Resolution: 1.47→36.83 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 1063 3.2 %
Rwork0.1593 32153 -
obs0.1606 33216 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.01 Å2 / Biso mean: 20.1737 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 1.47→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 49 248 1829
Biso mean--27.02 34.46 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.530.3241310.25013967409897
1.53-1.620.23451320.19763988412099
1.62-1.720.2671320.18023981411399
1.72-1.850.20081320.15344000413298
1.85-2.040.20941340.13240424176100
2.04-2.330.17381340.133840754209100
2.33-2.940.19011330.15734013414699
2.94-36.830.18591350.16074087422298

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