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- PDB-6sf7: Atomic resolution structure of SplF protease from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 6sf7
TitleAtomic resolution structure of SplF protease from Staphylococcus aureus
ComponentsSerine protease SplF
KeywordsHYDROLASE / Virulence factor / protease / bacterial
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B / Trypsin-like peptidase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine protease SplF
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGolik, P. / Stach, N. / Karim, A. / Dubin, G.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus .
Authors: Stach, N. / Karim, A. / Golik, P. / Kitel, R. / Pustelny, K. / Gruba, N. / Groborz, K. / Jankowska, U. / Kedracka-Krok, S. / Wladyka, B. / Drag, M. / Lesner, A. / Dubin, G.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Serine protease SplF
B: Serine protease SplF
C: Serine protease SplF
D: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,01423
Polymers88,1834
Non-polymers1,83119
Water8,107450
1
A: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5366
Polymers22,0461
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5887
Polymers22,0461
Non-polymers5426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4605
Polymers22,0461
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4305
Polymers22,0461
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.000, 58.580, 62.300
Angle α, β, γ (deg.)104.570, 95.310, 90.600
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine protease SplF


Mass: 22045.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: splF, SAUSA300_1753 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FFT4, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32.5 % PEG 400, 0.3 M Ammonium Sulphate pH = 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 77687 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 13.9 / Num. unique obs: 10882 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4VID

4vid


Resolution: 1.7→29.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.79 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3888 5 %RANDOM
Rwork0.1674 ---
obs0.1694 73794 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 27.698 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0.68 Å2-0.34 Å2
2---0.28 Å2-0.14 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.7→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 115 451 6463
Biso mean--52.97 35.51 -
Num. residues----789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0136237
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175570
X-RAY DIFFRACTIONr_angle_refined_deg2.051.6428483
X-RAY DIFFRACTIONr_angle_other_deg1.5831.57313017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.185809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62825.56259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.379156
X-RAY DIFFRACTIONr_chiral_restr0.1120.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021163
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 251 -
Rwork0.181 5239 -
all-5490 -
obs--88.15 %
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)
10.53870.0094-0.30931.444-0.07910.80880.0465-0.0152-0.07940.0665-0.0196-0.042-0.1630.0497-0.02690.0357-0.01050.00510.070.00590.029721.12233.71266.712
20.54870.20770.45511.31810.4511.97810.1035-0.03950.09440.0795-0.06120.04290.3655-0.173-0.04230.0703-0.0345-0.00920.05450.01350.0429-5.7175-24.12475.5848
31.28560.22220.53370.74810.1040.8342-0.0540.03990.037-0.04470.04810.053-0.06440.07880.0060.0405-0.0196-0.00870.0140.00460.00539.5504-6.6827-23.1922
41.82360.50440.22550.76440.0320.60580.02640.0775-0.02280.0916-0.0037-0.08870.021-0.0589-0.02270.0553-0.0241-0.0060.0260.00030.0139-15.0361-35.786-23.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 203
2X-RAY DIFFRACTION2B1 - 203
3X-RAY DIFFRACTION3C2 - 203
4X-RAY DIFFRACTION4D2 - 203

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