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- PDB-6yv6: Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Stap... -

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Basic information

Entry
Database: PDB / ID: 6yv6
TitleCrystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus
ComponentsSerine protease
KeywordsBIOSYNTHETIC PROTEIN / Spl / serine protease-like
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine protease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsRangel Pereira, M.R. / Brear, P. / Knyphausen, P. / Jermutus, L. / Hollfelder, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)695669 United Kingdom
CitationJournal: to be published
Title: Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus
Authors: Knyphausen, P. / Rangel Pereira, M.R. / Brear, P. / Jermutus, L. / Hollfelder, F.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2284
Polymers22,6451
Non-polymers5833
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint2 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.690, 44.310, 30.810
Angle α, β, γ (deg.)90.000, 92.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine protease


Mass: 22645.434 Da / Num. of mol.: 1 / Fragment: SPLB PROTEASE / Mutation: N2K/N3Q/S154R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: splB / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2D1PJH6, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.37 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350 30%, TRIS-Cl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.36→32.63 Å / Num. obs: 37738 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Net I/σ(I): 15.2 / Num. measured all: 271636 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.41.5271842528030.5570.6411.6621.199.4
6.08-32.630.02629724510.9990.0110.0295198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VID

2vid


Resolution: 1.36→19.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1912 5.07 %RANDOM
Rwork0.189 ---
obs0.19 37724 99.4 %-
Displacement parametersBiso max: 110.34 Å2 / Biso mean: 28.11 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1-5.16 Å20 Å20.7287 Å2
2---7.5589 Å20 Å2
3---2.399 Å2
Refinement stepCycle: final / Resolution: 1.36→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 36 113 1700
Biso mean--51.04 36.57 -
Num. residues----200
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d592SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes241HARMONIC5
X-RAY DIFFRACTIONt_it1667HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion212SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2085SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1667HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2245HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion4.53
X-RAY DIFFRACTIONt_other_torsion15.52
LS refinement shellResolution: 1.36→1.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2431 159 5.4 %
Rwork0.226 2788 -
all0.2269 2947 -
obs--99.35 %

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