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- PDB-7z9f: Human anionic trypsin after autoproteolysis at Arg122 -

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Basic information

Entry
Database: PDB / ID: 7z9f
TitleHuman anionic trypsin after autoproteolysis at Arg122
Components(Trypsin-2) x 2
KeywordsHYDROLASE / TRY2 / serine protease / autoproteolysis / digestion
Function / homology
Function and homology information


antimicrobial humoral response / Alpha-defensins / Antimicrobial peptides / Activation of Matrix Metalloproteinases / Collagen degradation / positive regulation of cell adhesion / collagen catabolic process / trypsin / extracellular matrix disassembly / digestion ...antimicrobial humoral response / Alpha-defensins / Antimicrobial peptides / Activation of Matrix Metalloproteinases / Collagen degradation / positive regulation of cell adhesion / collagen catabolic process / trypsin / extracellular matrix disassembly / digestion / serine-type peptidase activity / extracellular matrix / metalloendopeptidase activity / azurophil granule lumen / positive regulation of cell growth / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNagel, F. / Palm, G.J. / Delcea, M. / Lammers, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)637877European Union
CitationJournal: J Inflamm Res / Year: 2022
Title: Structural Basis of the Pancreatitis-Associated Autoproteolytic Failsafe Mechanism in Human Anionic Trypsin.
Authors: Nagel, F. / Susemihl, A. / Geist, N. / Mohlis, K. / Palm, G.J. / Lammers, M. / Delcea, M.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Trypsin-2
A: Trypsin-2
Y: Trypsin-2
B: Trypsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2386
Polymers48,1584
Non-polymers802
Water13,872770
1
X: Trypsin-2
Y: Trypsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1193
Polymers24,0792
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-43 kcal/mol
Surface area9820 Å2
2


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-85 kcal/mol
Surface area17870 Å2
3
A: Trypsin-2
B: Trypsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1193
Polymers24,0792
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-43 kcal/mol
Surface area9730 Å2
Unit cell
Length a, b, c (Å)59.060, 80.790, 87.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Trypsin-2 / Anionic trypsinogen / Serine protease 2 / Trypsin II


Mass: 11072.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS2, TRY2, TRYP2 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07478, trypsin
#2: Protein Trypsin-2 / Anionic trypsinogen / Serine protease 2 / Trypsin II


Mass: 13006.325 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS2, TRY2, TRYP2 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07478, trypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL protein (15 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl, 1 mM CaCl2) + 1 uL well solution (22% PEG 4000, 0.1 M Hepes pH 7.5, 0.1 M NaAc)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 9, 2021 / Details: DCM Si(111)
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 47119 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.169 / Rsym value: 0.162 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 7342 / CC1/2: 0.82 / Rrim(I) all: 1.252 / Rsym value: 1.203 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSVERSION Feb 5, 2021data reduction
XDSVERSION Feb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRN_A

Resolution: 1.7→47.68 Å / SU ML: 0.1549 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 1516 3.22 %
Rwork0.187 45524 -
obs0.188 47040 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 2 770 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643440
X-RAY DIFFRACTIONf_angle_d0.90234678
X-RAY DIFFRACTIONf_chiral_restr0.0642512
X-RAY DIFFRACTIONf_plane_restr0.0061616
X-RAY DIFFRACTIONf_dihedral_angle_d17.7046478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.26331300.23113902X-RAY DIFFRACTION95.09
1.75-1.810.27511350.22644066X-RAY DIFFRACTION99.95
1.81-1.890.27771380.22224132X-RAY DIFFRACTION99.98
1.89-1.970.25381370.21094113X-RAY DIFFRACTION99.77
1.97-2.080.22421370.19584119X-RAY DIFFRACTION99.91
2.08-2.210.21161370.18464130X-RAY DIFFRACTION99.84
2.21-2.380.21531390.18814149X-RAY DIFFRACTION99.79
2.38-2.620.21171370.18924126X-RAY DIFFRACTION99.84
2.62-2.990.23441380.18954186X-RAY DIFFRACTION99.93
2.99-3.770.1871410.16784220X-RAY DIFFRACTION99.84
3.77-47.680.20621470.17194381X-RAY DIFFRACTION99.43
Refinement TLS params.Method: refined / Origin x: -1.81458986763 Å / Origin y: 0.0222217079109 Å / Origin z: 8.6268521355 Å
111213212223313233
T0.100686823161 Å20.0168593554767 Å20.00524151772626 Å2-0.0834242969554 Å20.00534738229264 Å2--0.0876909091827 Å2
L0.38230959358 °20.0803998581143 °20.0695177137913 °2-0.189084145344 °20.0979027523142 °2--0.195212649796 °2
S-0.0192224983671 Å °-0.00479364644667 Å °-0.00510296173351 Å °0.00402497463132 Å °0.0101878294224 Å °0.0126340930777 Å °-0.0278423810289 Å °0.00465508084958 Å °0.000159665955469 Å °
Refinement TLS groupSelection details: all

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