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- PDB-6yv5: Crystal Structure of Serine protease SplB N3Q/S154R from Staphylo... -

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Basic information

Entry
Database: PDB / ID: 6yv5
TitleCrystal Structure of Serine protease SplB 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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 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 1.1Nov 30, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,6532
Polymers22,6301
Non-polymers231
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.920, 64.340, 73.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine protease /


Mass: 22630.357 Da / Num. of mol.: 1 / Fragment: SPLB PROTEASE / Mutation: 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.82 Å3/Da / Density % sol: 32.25 % / 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: 1.1→36.62 Å / Num. obs: 66249 / % possible obs: 97.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Net I/σ(I): 10.5 / Num. measured all: 336524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.1-1.132.50.726999540640.5520.5330.9071.182.4
4.92-36.625.60.0548778780.9980.0220.05529.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VID

2vid


Resolution: 1.1→24.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.967 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.039 / SU Rfree Blow DPI: 0.039 / SU Rfree Cruickshank DPI: 0.038
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3296 4.99 %RANDOM
Rwork0.186 ---
obs0.187 66027 97.5 %-
Displacement parametersBiso max: 104.27 Å2 / Biso mean: 19.25 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.3538 Å20 Å20 Å2
2---0.7668 Å20 Å2
3---0.413 Å2
Refinement stepCycle: final / Resolution: 1.1→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 1 197 1796
Biso mean--41.4 28.39 -
Num. residues----206
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d617SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes266HARMONIC5
X-RAY DIFFRACTIONt_it1752HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
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_contact2246SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1752HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2389HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion5.17
X-RAY DIFFRACTIONt_other_torsion15.08
LS refinement shellResolution: 1.1→1.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2369 220 5.41 %
Rwork0.2299 3849 -
all0.2303 4069 -
obs--81.69 %

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