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- PDB-7vo7: Crystal structure of trypsin in complex with Lima bean trypsin in... -

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Basic information

Entry
Database: PDB / ID: 7vo7
TitleCrystal structure of trypsin in complex with Lima bean trypsin inhibitor at 2.25A resolution.
Components
  • Bowman-Birk type proteinase inhibitor
  • Cationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / Trypsin Lima Bean complex / HYDROLASE-HYDROLASE INHIBITOR complex
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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Phaseolus lunatus (lima bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAhmad, M.S. / Akbar, Z. / Choudhary, M.I.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Other government Pakistan
CitationJournal: Proteins / Year: 2023
Title: Insight into the structural basis of the dual inhibitory mode of Lima bean (Phaseolus lunatus) serine protease inhibitor.
Authors: Ahmad, M.S. / Akbar, Z. / Choudhary, M.I.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Cationic trypsin
C: Bowman-Birk type proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53214
Polymers52,8063
Non-polymers72711
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-70 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.009, 54.009, 179.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein Bowman-Birk type proteinase inhibitor


Mass: 6157.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phaseolus lunatus (lima bean)

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Non-polymers , 5 types, 436 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1-0.4 M lithium sulfate, and 16% PEG-3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→17.98 Å / Num. obs: 24309 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.049 / Χ2: 1.17 / Net I/σ(I): 21.6
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1180 / CC1/2: 0.87 / Rrim(I) all: 0.238 / Χ2: 1.07 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SY3

6sy3


Resolution: 2.25→17.91 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1304 5.38 %
Rwork0.1809 --
obs0.1837 24229 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→17.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 41 425 4139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023782
X-RAY DIFFRACTIONf_angle_d0.5875125
X-RAY DIFFRACTIONf_dihedral_angle_d10.9851348
X-RAY DIFFRACTIONf_chiral_restr0.046577
X-RAY DIFFRACTIONf_plane_restr0.003657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.29551530.22712527X-RAY DIFFRACTION100
2.34-2.450.26941320.22032547X-RAY DIFFRACTION100
2.45-2.570.28831360.21522576X-RAY DIFFRACTION100
2.58-2.740.26311750.20052491X-RAY DIFFRACTION100
2.74-2.950.30581330.19962566X-RAY DIFFRACTION100
2.95-3.240.25051680.18322510X-RAY DIFFRACTION100
3.24-3.710.22991400.15212547X-RAY DIFFRACTION100
3.71-4.650.15591340.14222572X-RAY DIFFRACTION100
4.66-17.910.181330.17362589X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5429-0.1993-0.26181.2839-0.34981.2341-0.0798-0.07850.01030.09250.0858-0.013-0.0050.0173-0.01370.11720.0088-0.03920.07140.00130.087119.726423.33136.1288
20.768-0.14270.18990.75790.48091.9896-0.02730.10360.12820.05930.0194-0.1915-0.13810.3712-0.07060.1178-0.0454-0.04590.11-0.00190.163328.790426.92873.3992
33.0351-0.6682-0.54752.15080.11146.83090.240.1419-0.552-0.6283-0.120.15270.7246-0.8724-0.16290.2674-0.0295-0.0530.1335-0.00680.166217.28669.6847-1.8504
41.334-0.1297-0.1710.79-0.32861.46910.09390.09710.0557-0.0723-0.0455-0.09460.06910.0718-0.03840.1171-0.005-0.01350.09060.04330.093321.620226.4642-8.9519
51.1915-0.06990.42580.5721-0.08831.5166-0.0061-0.00960.07320.02150.04050.0071-0.1328-0.0434-0.02680.07570.0085-0.00690.10740.03450.091-3.604746.6516-33.7887
61.1075-0.1054-0.11920.7709-0.29092.5663-0.00640.03170.13640.0732-0.0037-0.103-0.37140.10160.01630.0948-0.0325-0.01110.09170.00480.1681-0.057455.8909-31.1364
74.0764-0.59180.4973.0382.34843.0428-0.0758-0.2128-0.24870.05170.12340.59280.5262-0.5194-0.09840.1226-0.0012-0.00360.21870.04170.2157-17.321244.2532-25.9285
80.8295-0.3623-0.07380.70990.10331.50730.0004-0.21250.1230.07370.0312-0.0379-0.0718-0.0516-0.00040.08430.0044-0.03960.11550.00590.1257-0.550148.6332-18.8826
91.488-0.31.8261.2106-0.99973.9360.4141-0.6273-0.55390.0001-0.00440.1270.7102-0.3993-0.30190.2753-0.0927-0.08750.37830.12130.3383-2.860427.746-15.0997
100.3187-0.20910.49020.2021-0.53421.4513-0.0091-0.1426-0.0121-0.32090.29160.28960.407-0.5026-0.14430.3048-0.0972-0.17070.30370.14680.3230.644724.4598-11.708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 246 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 103 )
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 140 )
7X-RAY DIFFRACTION7chain 'B' and (resid 141 through 155 )
8X-RAY DIFFRACTION8chain 'B' and (resid 156 through 246 )
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 48 )
10X-RAY DIFFRACTION10chain 'C' and (resid 49 through 72 )

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