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- PDB-9qfv: Human Tryptase beta-2 (hTPSB2) -

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Basic information

Entry
Database: PDB / ID: 9qfv
TitleHuman Tryptase beta-2 (hTPSB2)
ComponentsTryptase beta-2
KeywordsHYDROLASE / BETA-TRYPTASE
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / : / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
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
ACETATE ION / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPorta, A. / Manelfi, C. / Talarico, C. / Beccari, A.R. / Brindisi, M. / Summa, V. / Iaconis, D. / Gobbi, M. / Beeg, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2025
Title: Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors.
Authors: Porta, A. / Manelfi, C. / Talarico, C. / Beccari, A.R. / Brindisi, M. / Summa, V. / Iaconis, D. / Gobbi, M. / Beeg, M.
History
DepositionMar 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptase beta-2
B: Tryptase beta-2
C: Tryptase beta-2
D: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,40339
Polymers109,9664
Non-polymers3,43735
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.634, 78.634, 165.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tryptase beta-2 / Tryptase-2 / Tryptase II


Mass: 27491.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Lung / References: UniProt: P20231, tryptase

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Non-polymers , 7 types, 589 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.06→68.1 Å / Num. obs: 70311 / % possible obs: 99.95 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 8.2
Reflection shellResolution: 2.06→2.094 Å / Num. unique obs: 70696 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
REFMACv.5refinement
autoPROCdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→68.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.89 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21921 365 21.9 %RANDOM
Rwork0.18825 ---
obs0.18842 70311 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.788 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.06→68.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7715 0 212 554 8481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138179
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177462
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.64311208
X-RAY DIFFRACTIONr_angle_other_deg1.1391.57117204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89551002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2721.974390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.487151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0631543
X-RAY DIFFRACTIONr_chiral_restr0.0610.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210744
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021814
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7433.8533937
X-RAY DIFFRACTIONr_mcbond_other1.7333.8513932
X-RAY DIFFRACTIONr_mcangle_it2.5955.7794918
X-RAY DIFFRACTIONr_mcangle_other2.5955.784919
X-RAY DIFFRACTIONr_scbond_it2.1774.194242
X-RAY DIFFRACTIONr_scbond_other2.1764.194243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3596.1616277
X-RAY DIFFRACTIONr_long_range_B_refined5.72244.9978676
X-RAY DIFFRACTIONr_long_range_B_other5.69244.8278617
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27510.03
12B27510.03
21A27880.01
22C27880.01
31A27320.03
32D27320.03
41B27380.03
42C27380.03
51B27980.02
52D27980.02
61C27100.03
62D27100.03
LS refinement shellResolution: 2.06→2.112 Å
RfactorNum. reflection% reflection
Rfree0.293 27 -
Rwork0.295 5184 -
obs--99.75 %

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