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- PDB-6e0u: Staphylococcus pseudintermedius exfoliative toxin EXI -

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Basic information

Entry
Database: PDB / ID: 6e0u
TitleStaphylococcus pseudintermedius exfoliative toxin EXI
ComponentsSerine protease
KeywordsHYDROLASE / TOXIN / exfoliative toxin / exi / Staphylococcus pseudintermedius
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / : / serine-type endopeptidase activity
Similarity search - Function
Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus pseudintermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsBoone, C.D. / Laganowsky, A.
CitationJournal: To be Published
Title: Crystal structure of the Exfoliative toxin Exi from Staphylococcus pseudintermedius
Authors: Boone, C.D. / Liu, W. / Laganowsky, A. / Hook, A.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Serine protease
B: Serine protease


Theoretical massNumber of molelcules
Total (without water)54,3492
Polymers54,3492
Non-polymers00
Water543
1
A: Serine protease


Theoretical massNumber of molelcules
Total (without water)27,1751
Polymers27,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease


Theoretical massNumber of molelcules
Total (without water)27,1751
Polymers27,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.230, 82.130, 99.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid CZ00

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segid CZ00B0

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Components

#1: Protein Serine protease / / Exfoliative toxin Exi


Mass: 27174.715 Da / Num. of mol.: 2 / Fragment: UNP residues 33-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus pseudintermedius (bacteria)
Gene: exi / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D0VXY8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM ammonium sulfate, 100 mM Tris, pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→63.355 Å / Num. obs: 14511 / % possible obs: 99 % / Redundancy: 5.935 % / Biso Wilson estimate: 56.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.093 / Χ2: 1.044 / Net I/σ(I): 12.38 / Num. measured all: 86124 / Scaling rejects: 150
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.823.5480.2962.3210040.9560.34795.7
2.82-2.95.9030.2663.9710190.9790.2997.7
2.9-2.986.6040.2085.389990.9880.22699.8
2.98-3.076.6080.1946.099910.9890.21199.4
3.07-3.186.4240.1846.589460.990.299.7
3.18-3.296.1750.1738.029160.9880.1999.7
3.29-3.415.9130.1469.688900.990.16199
3.41-3.556.2920.1211.768560.9920.131100
3.55-3.716.1420.10613.218240.9950.11698.9
3.71-3.895.9440.09215.097870.9920.10199.4
3.89-4.15.5370.08816.387410.9930.09899.3
4.1-4.355.8410.07918.167110.9920.08798.9
4.35-4.656.1590.06920.386720.9960.07699.4
4.65-5.026.1490.06520.626430.9960.07199.2
5.02-5.55.70.06120.135730.9950.06898.8
5.5-6.156.4080.059215340.9980.06599.4
6.15-7.16.2240.05621.594730.9970.06199.4
7.1-8.75.6660.05622.234070.9970.06299.3
8.7-12.36.030.05725.333280.9960.062100
12.3-63.3555.1520.0623.131970.9960.06697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.08 Å63.36 Å
Translation7.08 Å63.36 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QTF

1qtf


Resolution: 2.75→63.355 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 38.67
RfactorNum. reflection% reflection
Rfree0.3256 726 5.01 %
Rwork0.2844 --
obs0.2864 14486 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.29 Å2 / Biso mean: 60.867 Å2 / Biso min: 57.44 Å2
Refinement stepCycle: final / Resolution: 2.75→63.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 0 3 3432
Biso mean---61.3 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033505
X-RAY DIFFRACTIONf_angle_d0.8544799
X-RAY DIFFRACTIONf_chiral_restr0.032559
X-RAY DIFFRACTIONf_plane_restr0.005638
X-RAY DIFFRACTIONf_dihedral_angle_d12.741164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1926X-RAY DIFFRACTION6.079TORSIONAL
12B1926X-RAY DIFFRACTION6.079TORSIONAL
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 (%)
2.75-2.96240.40561400.38532641278197
2.9624-3.26050.40091430.36592723286699
3.2605-3.73220.40611450.31492736288199
3.7322-4.7020.30471450.25612766291199
4.702-63.37190.27081530.24712894304799

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