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- PDB-7bs5: Bovine Pancreatic Trypsin with 6-Methoxytryptamine (Cryo) -

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Basic information

Entry
Database: PDB / ID: 7bs5
TitleBovine Pancreatic Trypsin with 6-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-(6-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: 1.17 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 1.3Oct 30, 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)23,7896
Polymers23,3241
Non-polymers4655
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.841, 56.901, 66.570
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-F5X / 2-(6-methoxy-1H-indol-3-yl)ethanamine / 6-Methoxytryptamine


Mass: 190.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
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: 1.17→39.49 Å / Num. obs: 134160 / % possible obs: 99.2 % / Redundancy: 7.223 % / Biso Wilson estimate: 15.448 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.082 / Χ2: 1.03 / Net I/σ(I): 15.39 / Num. measured all: 969101
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
1.17-1.245.8021.1281.4412097021922208490.5411.24195.1
1.24-1.337.3110.7472.615028820558205570.7920.804100
1.33-1.437.4030.4594.3314161719130191290.9180.493100
1.43-1.577.490.2517.9113180717597175970.9770.27100
1.57-1.767.5650.1413.8912069215955159540.9930.151100
1.76-2.037.5930.07325.0110646714023140220.9980.078100
2.03-2.487.5450.04738.048942711854118520.9990.05100
2.48-3.57.5610.03548.4369217915491540.9990.037100
3.5-39.497.6530.03157.9238616505350460.9990.03399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.39 Å39.49 Å
Translation5.39 Å39.49 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: 1.17→39.49 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.19
RfactorNum. reflection% reflection
Rfree0.1801 6980 5.2 %
Rwork0.1666 --
obs0.1673 134153 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.79 Å2 / Biso mean: 15.061 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 1.17→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 59 360 2048
Biso mean--16.98 25.8 -
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 (%)
1.17-1.190.27932400.29983620386086
1.19-1.20.31212020.29914059426193
1.2-1.210.29022680.28274124439298
1.21-1.230.28332350.259942204455100
1.23-1.250.24361940.247943184512100
1.25-1.260.23571700.231343234493100
1.26-1.280.24391710.236643274498100
1.28-1.30.20612180.221643214539100
1.3-1.320.25952000.216143044504100
1.32-1.340.23462560.207642444500100
1.34-1.360.222800.206642044484100
1.36-1.390.22712460.194543174563100
1.39-1.420.20432350.184542724507100
1.42-1.440.21422210.179242334454100
1.44-1.480.20762800.159442384518100
1.48-1.510.15172090.161443074516100
1.51-1.550.16762070.157343064513100
1.55-1.590.16741990.153343084507100
1.59-1.640.18622340.150642354469100
1.64-1.690.15682450.147742964541100
1.69-1.750.19692170.160442914508100
1.75-1.820.17392660.162942324498100
1.82-1.90.19892380.163942864524100
1.9-20.16662740.150342204494100
2-2.130.16412240.147142964520100
2.13-2.290.15812440.154742714515100
2.29-2.520.18882410.157242474488100
2.52-2.890.16972600.161442514511100
2.89-3.640.15532560.144842484504100
3.64-39.490.14662500.142642554505100

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