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- PDB-8d4v: Crystal Structure of Cathepsin G Inhibited by Eap2 from S. aureus -

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Basic information

Entry
Database: PDB / ID: 8d4v
TitleCrystal Structure of Cathepsin G Inhibited by Eap2 from S. aureus
Components
  • Cathepsin G, C-terminal truncated form
  • Extracellular Adherence Protein
KeywordsHYDROLASE/INHIBITOR / PROTEIN BINDING / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus / HYDROLASE-INHIBITOR / PROTEIN BINDING complex
Function / homology
Function and homology information


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / Activation of Matrix Metalloproteinases / monocyte chemotaxis / extracellular matrix disassembly / defense response to fungus / Purinergic signaling in leishmaniasis infection / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / protein maturation / positive regulation of immune response / protein processing / platelet activation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / : / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / protein phosphorylation / lysosome / defense response to Gram-positive bacterium / immune response / receptor ligand activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease ...MAP domain / MAP domain / MAP repeat profile. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Cathepsin G / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsGido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family.
Authors: Gido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
History
DepositionJun 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin G, C-terminal truncated form
C: Cathepsin G, C-terminal truncated form
B: Extracellular Adherence Protein
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0336
Polymers72,8414
Non-polymers1922
Water4,035224
1
A: Cathepsin G, C-terminal truncated form
B: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5173
Polymers36,4212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-19 kcal/mol
Surface area15500 Å2
MethodPISA
2
C: Cathepsin G, C-terminal truncated form
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5173
Polymers36,4212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-19 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.561, 80.273, 99.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Cathepsin G, C-terminal truncated form


Mass: 25397.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Purified from human sputum / Tissue: Neutrophil / References: UniProt: P08311
#2: Protein Extracellular Adherence Protein / Protein map


Mass: 11023.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: map, SAV1938 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BisTris (pH 6.5), 0.2M Ammonium Sulfate, 25%(w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 53684 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 32.64 Å2 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.075 / Rrim(I) all: 0.253 / Χ2: 1.015 / Net I/σ(I): 7.9 / Num. measured all: 544796
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.81.94652970.5170.7592.0941.03199.6
1.92-1.998.11.59552930.7010.5661.6951.05799.5
1.99-2.088.31.12752410.7920.4031.21.04299
2.08-2.1910.20.94953310.8890.2990.9961.05799.8
2.19-2.3311.30.70653440.9470.2120.7381.04899.8
2.33-2.5111.50.51253530.9680.1540.5351.01999.9
2.51-2.7611.20.35853640.9770.110.3740.99899.9
2.76-3.1610.70.19253560.9880.060.2010.99599
3.16-3.9912.10.1354640.9920.0390.1360.961100
3.99-50110.24556410.9680.0760.2570.97699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CGH, 1YN3

1cgh

1yn3


Resolution: 1.85→37.24 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 1874 3.74 %
Rwork0.2074 48231 -
obs0.209 50105 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.44 Å2 / Biso mean: 44.2925 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: final / Resolution: 1.85→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 10 224 5312
Biso mean--50.04 46.65 -
Num. residues----641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90.41481250.33233083320879
1.9-1.960.34571300.29963294342483
1.96-2.020.29351230.26533406352987
2.02-2.090.35361370.24223494363188
2.09-2.170.28581410.2323649379092
2.17-2.270.28431370.22113684382194
2.27-2.390.24591460.21383780392696
2.39-2.540.2661540.21453832398697
2.54-2.740.29011490.22633878402797
2.74-3.020.25581540.22653918407298
3.02-3.450.24651510.209539934144100
3.45-4.350.20491620.172340594221100
4.35-37.240.23571650.19214161432698

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