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- PDB-8e7f: Crystal structure of the autotransporter Ssp from Serratia marcescens. -

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Basic information

Entry
Database: PDB / ID: 8e7f
TitleCrystal structure of the autotransporter Ssp from Serratia marcescens.
ComponentsExtracellular serine protease
KeywordsHYDROLASE / autotransporter / subtilase / Serratia. / Toxin
Function / homology
Function and homology information


outer membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Autotransporter serine protease peptidase domain / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Pectin lyase fold/virulence factor ...Autotransporter serine protease peptidase domain / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Pectin lyase fold/virulence factor / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / Extracellular serine protease
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsHor, L. / Pilapitiya, A. / Panjikar, S. / Paxman, J.J. / Heras, B.
Funding support Australia, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150102287 Australia
Australian Research Council (ARC)DP180102987 Australia
Australian Research Council (ARC)DP210100673 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1143638 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structure of a subtilisin-like autotransporter passenger domain reveals insights into its cytotoxic function.
Authors: Hor, L. / Pilapitiya, A. / McKenna, J.A. / Panjikar, S. / Anderson, M.A. / Desvaux, M. / Paxman, J.J. / Heras, B.
History
DepositionAug 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,34314
Polymers66,0791
Non-polymers1,26413
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.482, 55.356, 61.883
Angle α, β, γ (deg.)91.520, 93.040, 102.760
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular serine protease


Mass: 66078.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P09489, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Non-polymers , 5 types, 320 molecules

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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M potassium iodide, 20% (w/v) PEG 3350, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537, 0.9642
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2019
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.96421
ReflectionResolution: 2→46.2 Å / Num. obs: 39914 / % possible obs: 97.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2 / Num. unique obs: 5596 / CC1/2: 0.774 / Rpim(I) all: 0.405 / Rrim(I) all: 0.724 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
Coot0.9.5model building
XDS2022data scaling
Auto-Rickshaw2022phasing
BUCCANEERphasing
SHELXCDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→39.89 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.202 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2033 5.1 %RANDOM
Rwork0.1633 ---
obs0.1653 37873 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.15 Å2 / Biso mean: 39.742 Å2 / Biso min: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å22.09 Å2-1.99 Å2
2---1.96 Å20.1 Å2
3----3.51 Å2
Refinement stepCycle: final / Resolution: 2→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 34 307 4945
Biso mean--59.95 45.03 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174382
X-RAY DIFFRACTIONr_angle_refined_deg1.461.6366460
X-RAY DIFFRACTIONr_angle_other_deg1.3331.58110054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92422.112251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99615730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8111534
X-RAY DIFFRACTIONr_chiral_restr0.0610.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021152
LS refinement shellResolution: 2.005→2.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 136 -
Rwork0.297 2610 -
all-2746 -
obs--89.65 %

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