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- PDB-30zu: Bovine trypsin inhibited by PMSF. -

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Basic information

Entry
Database: PDB / ID: 30zu
TitleBovine trypsin inhibited by PMSF.
ComponentsCationic Trypsin
KeywordsHYDROLASE / inhibitor
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / : / proteolysis / 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. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / 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. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / 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
phenylmethanesulfonic acid / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBloch, Y.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
Citation
Journal: To Be Published
Title: Observation of sulfonylation elimination products by crystallography.
Authors: Bloch, Y. / Panneerselvam, S.
#1: Journal: Biophys.Struct.Mech. / Year: 1975
Title: The structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor III. Structure of the anhydro-trypsin-inhibitor complex.
Authors: Huber, R. / Bode, W. / Kukla, D. / Kohl, U. / Ryan, C.A.
#2: Journal: Nature / Year: 2025
Title: SuFEx-based antitubercular compound irreversibly inhibits Pks13.
Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / ...Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / Gambacurta, J. / Hvizdos, J. / Reagan, M. / Jones, I.L. / Massoudi, L.M. / Woolhiser, L.K. / Cascioferro, A. / Kundrick, E. / Singh, P. / Reiley, W. / Ioerger, T.R. / Kandula, D.R. / McCabe, J.W. / Guo, T. / Alland, D. / Boshoff, H.I. / Schnappinger, D. / Robertson, G.T. / Mdluli, K. / Lee, K.J. / Dong, J. / Li, S. / Schultz, P.G. / Joseph, S.B. / Love, M.S. / Sharpless, K.B. / Petrassi, H.M. / Chatterjee, A.K. / Sacchettini, J.C. / McNamara, C.W.
History
DepositionMay 19, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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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)26,0183
Polymers25,8061
Non-polymers2122
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-10 kcal/mol
Surface area9040 Å2
Unit cell
Length a, b, c (Å)54.582, 58.161, 66.644
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic Trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues [1-23] are signal and propeptide which are cleaved during protein maturation.
Source: (natural) Bos taurus (domestic cattle) / Organ: Pancreas / Plasmid details: Sigma T1426 / 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-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 8000, 50 mM HEPES pH 7.0, 0.2 M Ammonium sulfate, 3 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 0.987→43.82 Å / Num. obs: 106327 / % possible obs: 98.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 8.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Net I/σ(I): 14.2
Reflection shell

Num. unique obs: 5316 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.844-43.8213.50.037580.9990.010.038100
0.987-1.04314.22.0211.30.60.5532.09675.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC2025-04-07data reduction
XDS20250430data reduction
STARANISO3.0.6data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→24.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.02 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.021 / SU Rfree Blow DPI: 0.023 / SU Rfree Cruickshank DPI: 0.021
RfactorNum. reflection% reflectionSelection details
Rfree0.1396 4827 -RANDOM
Rwork0.1186 ---
obs0.1195 99291 99.9 %-
Displacement parametersBiso mean: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.0617 Å20 Å20 Å2
2---0.0052 Å20 Å2
3----0.0565 Å2
Refine analyzeLuzzati coordinate error obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.05→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 11 313 1953
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153676HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.126660HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d1139SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes624HARMONIC5
X-RAY DIFFRACTIONt_it3665HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion250SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies25HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3903SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.81
X-RAY DIFFRACTIONt_other_torsion16.1
LS refinement shellResolution: 1.05→1.06 Å
RfactorNum. reflection% reflection
Rfree0.2273 93 -
Rwork0.2317 --
obs0.2315 1986 95.8 %

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