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- PDB-7bs4: Bovine Pancreatic Trypsin with 5-Methoxytryptamine (Cryo) -

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Basic information

Entry
Database: PDB / ID: 7bs4
TitleBovine Pancreatic Trypsin with 5-Methoxytryptamine (Cryo)
ComponentsCationic trypsin
KeywordsHYDROLASE / microfluidic device / crystal sorting / room temperature
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
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 ...: / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-(5-methoxy-1H-indol-3-yl)ethanamine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.04 Å
AuthorsMaeki, M. / Ito, S. / Takeda, R. / Funakubo, T. / Ueno, G. / Ishida, A. / Tani, H. / Yamamoto, M. / Tokeshi, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Chem Sci / Year: 2020
Title: Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis.
Authors: Maeki, M. / Ito, S. / Takeda, R. / Ueno, G. / Ishida, A. / Tani, H. / Yamamoto, M. / Tokeshi, M.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1369
Polymers23,3241
Non-polymers8118
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.559, 58.673, 66.505
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 Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-F5U / 2-(5-methoxy-1H-indol-3-yl)ethanamine / 5-Methoxytryptamine


Mass: 190.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.04→33.25 Å / Num. obs: 172721 / % possible obs: 86.4 % / Redundancy: 6.258 % / Biso Wilson estimate: 12.085 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.032 / Χ2: 1.05 / Net I/σ(I): 31.94 / Num. measured all: 1080974
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.04-1.12.3060.2892.692385732373103440.8460.38332
1.1-1.183.180.1586.138096430375254630.9610.19283.8
1.18-1.276.0820.12412.917181128301282490.990.13699.8
1.27-1.397.3370.08620.7819047725962259620.9970.092100
1.39-1.557.4190.05232.7917462123536235360.9990.056100
1.55-1.797.4490.03547.4215459020754207540.9990.038100
1.79-2.27.410.02762.8312972817513175070.9990.029100
2.2-3.17.4180.02372.97100485135471354710.025100
3.1-33.257.3980.01979.34544417490735910.02198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.33 Å33.25 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.17refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s0q

1s0q


Resolution: 1.04→33.25 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.66
RfactorNum. reflection% reflection
Rfree0.1719 8705 5.04 %
Rwork0.154 --
obs0.1549 172719 86.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.01 Å2 / Biso mean: 12.9886 Å2 / Biso min: 5.72 Å2
Refinement stepCycle: final / Resolution: 1.04→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 135 415 2179
Biso mean--17.14 23.18 -
Num. residues----223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.04-1.050.2631230.31565095328
1.05-1.060.2499760.27431261133720
1.06-1.070.23591130.24252085219833
1.07-1.090.21231460.21432921306746
1.09-1.10.18932060.19113572377857
1.1-1.120.19262330.18194400463369
1.12-1.130.17982350.16925097533280
1.13-1.150.16323010.16475661596289
1.15-1.170.16212600.16415988624895
1.17-1.190.16173500.15966225657598
1.19-1.210.16472940.153763826676100
1.21-1.230.18232980.156163616659100
1.23-1.250.17843080.154463516659100
1.25-1.280.14563250.157363186643100
1.28-1.310.16193730.161663146687100
1.31-1.340.17213000.160463486648100
1.34-1.370.16853790.15662686647100
1.37-1.410.18263510.153863316682100
1.41-1.450.14733800.144562506630100
1.45-1.50.18913090.145563306639100
1.5-1.550.14713520.143463486700100
1.55-1.610.1642800.142663476627100
1.61-1.680.15723100.145663696679100
1.68-1.770.16793680.151762926660100
1.77-1.880.16433590.153363026661100
1.88-2.030.17973580.150562826640100
2.03-2.230.16453830.149162736656100
2.23-2.560.19183190.158763626681100
2.56-3.220.17073790.162662646643100
3.22-33.250.17933370.14386203654098

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