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- PDB-7brv: Bovine Pancreatic Trypsin with 4-Bromobenzamidine (Room Temperature) -

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Basic information

Entry
Database: PDB / ID: 7brv
TitleBovine Pancreatic Trypsin with 4-Bromobenzamidine (Room Temperature)
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
4-bromanylbenzenecarboximidamide / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsTakeda, R. / Ito, S. / Maeki, M. / 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

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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)23,8346
Polymers23,3241
Non-polymers5095
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.980, 58.770, 68.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-F5R / 4-bromanylbenzenecarboximidamide / 4-Bromobenzamidine


Mass: 199.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BrN2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.55→44.47 Å / Num. obs: 61294 / % possible obs: 99.2 % / Redundancy: 5.458 % / Biso Wilson estimate: 22.481 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.187 / Χ2: 0.985 / Net I/σ(I): 10.13 / Num. measured all: 334521 / Scaling rejects: 1636
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
1.55-1.645.2331.9161.8649734958395040.3152.12999.2
1.64-1.765.3161.1562.9352614996398980.5951.28299.3
1.76-1.95.3920.6155.0146428868886110.8410.68199.1
1.9-2.085.4710.338.3443257796479060.9490.36499.3
2.08-2.335.5250.20612.2140491738673290.9740.22799.2
2.33-2.685.5710.14915.3634508623961940.9850.16499.3
2.68-3.295.6530.09819.6630938550954730.9930.10799.3
3.29-4.655.720.06126.9623572416841210.9960.06798.9
4.65-44.475.7480.05927.4112979229322580.9960.06498.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.3 Å44.47 Å

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Processing

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

1s0q


Resolution: 1.55→44.47 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 3139 5.13 %
Rwork0.1549 58064 -
obs0.1557 61203 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.98 Å2 / Biso mean: 18.4068 Å2 / Biso min: 7.43 Å2
Refinement stepCycle: final / Resolution: 1.55→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 38 163 1830
Biso mean--31.06 31.28 -
Num. residues----223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.25331260.26162656278299
1.57-1.60.28541510.24922543269498
1.6-1.630.24061270.24792665279299
1.63-1.660.24361330.23532639277299
1.66-1.690.25171250.2292657278299
1.69-1.720.23361780.20662660283899
1.72-1.760.22341740.20732576275099
1.76-1.80.19421230.1892652277599
1.8-1.850.24791200.18622682280299
1.85-1.90.19381190.16562672279199
1.9-1.950.19031450.16162660280599
1.95-2.020.17381690.15342575274499
2.02-2.090.15391620.14822643280599
2.09-2.170.17981390.13732634277399
2.17-2.270.18041520.14232644279699
2.27-2.390.17011480.14072639278799
2.39-2.540.15231480.14592644279299
2.54-2.740.14191330.14162659279299
2.74-3.010.15771260.15722672279899
3.01-3.450.15111350.13472648278399
3.45-4.340.12551460.11412627277399
4.34-44.470.15021600.13692617277799

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