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- PDB-7wb8: Crystal structure of Bovine Pancreatic Trypsin in complex with 5-... -

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Basic information

Entry
Database: PDB / ID: 7wb8
TitleCrystal structure of Bovine Pancreatic Trypsin in complex with 5-Methoxytryptamine at Room Temperature
ComponentsCationic trypsin
KeywordsHYDROLASE
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 / Resolution: 1.38 Å
AuthorsSakai, N. / Okumura, H. / Yamamoto, M. / Kumasaka, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: In situ crystal data-collection and ligand-screening system at SPring-8.
Authors: Okumura, H. / Sakai, N. / Murakami, H. / Mizuno, N. / Nakamura, Y. / Ueno, G. / Masunaga, T. / Kawamura, T. / Baba, S. / Hasegawa, K. / Yamamoto, M. / Kumasaka, T.
History
DepositionDec 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6334
Polymers23,3241
Non-polymers3083
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 58.380, 67.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-F5U / 2-(5-methoxy-1H-indol-3-yl)ethanamine / 5-Methoxytryptamine


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 44589 / % possible obs: 99.3 % / Redundancy: 4.97 % / Biso Wilson estimate: 15.4 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.09 / Net I/σ(I): 11.12
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 4.98 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6834 / CC1/2: 0.528 / Rrim(I) all: 1.294 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S0R

1s0r


Resolution: 1.38→44.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.119 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16521 2224 5 %RANDOM
Rwork0.13015 ---
obs0.13192 42442 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å20 Å2
2--1.72 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.38→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 19 118 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181554
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6222287
X-RAY DIFFRACTIONr_angle_other_deg1.6141.5783593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3425.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74615269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.981152
X-RAY DIFFRACTIONr_chiral_restr0.1120.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
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_it2.1911.467891
X-RAY DIFFRACTIONr_mcbond_other2.191.467890
X-RAY DIFFRACTIONr_mcangle_it2.7242.2331112
X-RAY DIFFRACTIONr_mcangle_other2.7242.2331113
X-RAY DIFFRACTIONr_scbond_it3.711.893793
X-RAY DIFFRACTIONr_scbond_other3.7081.894794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.272.6371176
X-RAY DIFFRACTIONr_long_range_B_refined4.06118.7341879
X-RAY DIFFRACTIONr_long_range_B_other4.0218.6781873
X-RAY DIFFRACTIONr_rigid_bond_restr3.67533238
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 155 -
Rwork0.408 3095 -
obs--99.3 %

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