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- PDB-7al8: Structure of ATSI with bovine trypsin -

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Basic information

Entry
Database: PDB / ID: 7al8
TitleStructure of ATSI with bovine trypsin
Components
  • Cationic trypsin
  • Trypsin/subtilisin inhibitor
KeywordsHYDROLASE / ATSI / trypsin / inhibitor
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / 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. ...Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / 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
Serine protease 1 / Trypsin/subtilisin inhibitor
Similarity search - Component
Biological speciesAmaranthus caudatus (amaranth)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsReverter, D. / Covaleda, G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: To Be Published
Title: Structure of ATSI with bovine trypsin
Authors: Reverter, D. / Covaleda, G.
History
DepositionOct 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
U: Cationic trypsin
X: Trypsin/subtilisin inhibitor
B: Cationic trypsin
C: Trypsin/subtilisin inhibitor
E: Cationic trypsin
F: Trypsin/subtilisin inhibitor
H: Cationic trypsin
I: Trypsin/subtilisin inhibitor
K: Cationic trypsin
L: Trypsin/subtilisin inhibitor
N: Cationic trypsin
O: Trypsin/subtilisin inhibitor
Q: Cationic trypsin
R: Trypsin/subtilisin inhibitor
T: Cationic trypsin
V: Trypsin/subtilisin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,37245
Polymers249,81016
Non-polymers2,56229
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24800 Å2
ΔGint-384 kcal/mol
Surface area90570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.289, 92.588, 108.545
Angle α, β, γ (deg.)90.040, 89.860, 90.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein
Trypsin/subtilisin inhibitor / ATSI


Mass: 7901.974 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amaranthus caudatus (amaranth) / Production host: Escherichia coli (E. coli) / References: UniProt: P80211
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 46.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 2M AmSO4, 0.1 M HEPES 7.5; 2% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.84→46.84 Å / Num. obs: 50831 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.101 / Net I/σ(I): 4.4
Reflection shellResolution: 2.84→2.99 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 6984 / Rpim(I) all: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
SCALAdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQ7

1aq7


Resolution: 2.85→46.84 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 40.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3305 2563 5.08 %
Rwork0.2744 47892 -
obs0.2772 50455 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.98 Å2 / Biso mean: 46.173 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 2.85→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17352 0 129 0 17481
Biso mean--70.05 --
Num. residues----2320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.90.47151330.38822568270194
2.9-2.960.4041550.33432598275396
2.96-3.030.42841200.33332700282096
3.03-3.10.38291510.32912632278396
3.1-3.180.44661550.33062637279297
3.18-3.260.40631480.31792637278597
3.26-3.360.41461340.31472680281497
3.36-3.470.35471160.29232736285297
3.47-3.590.371570.29692701285898
3.59-3.730.32131320.2692656278897
3.73-3.90.31481430.25532659280297
3.9-4.110.28371560.24632662281897
4.11-4.370.27951470.23162716286398
4.37-4.70.28731380.25022650278897
4.7-5.180.33431390.23512677281697
5.18-5.920.311480.2552672282097
5.93-7.460.27981310.25072660279197
7.46-46.840.26981600.26292651281197
Refinement TLS params.Method: refined / Origin x: -5.333 Å / Origin y: 3.816 Å / Origin z: 8.7089 Å
111213212223313233
T0.2581 Å20.0071 Å2-0.0169 Å2-0.3109 Å20.0507 Å2--0.2975 Å2
L0.3313 °20.0079 °2-0.0996 °2-0.0435 °20.0397 °2--0.2966 °2
S-0.0143 Å °0.1001 Å °-0.0368 Å °0.0044 Å °0.029 Å °-0.0298 Å °0.0208 Å °-0.0606 Å °-0.0155 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLU24 - 246
2X-RAY DIFFRACTION1ALLU301
3X-RAY DIFFRACTION1ALLX2 - 68
4X-RAY DIFFRACTION1ALLX101 - 102
5X-RAY DIFFRACTION1ALLB24 - 246
6X-RAY DIFFRACTION1ALLB301
7X-RAY DIFFRACTION1ALLC2 - 68
8X-RAY DIFFRACTION1ALLC101 - 102
9X-RAY DIFFRACTION1ALLE24 - 246
10X-RAY DIFFRACTION1ALLE301 - 302
11X-RAY DIFFRACTION1ALLF2 - 68
12X-RAY DIFFRACTION1ALLF101 - 102
13X-RAY DIFFRACTION1ALLH24 - 246
14X-RAY DIFFRACTION1ALLH301 - 302
15X-RAY DIFFRACTION1ALLI2 - 68
16X-RAY DIFFRACTION1ALLI101 - 102
17X-RAY DIFFRACTION1ALLK24 - 246
18X-RAY DIFFRACTION1ALLK301
19X-RAY DIFFRACTION1ALLL2 - 68
20X-RAY DIFFRACTION1ALLL101 - 102
21X-RAY DIFFRACTION1ALLN24 - 246
22X-RAY DIFFRACTION1ALLN301 - 302
23X-RAY DIFFRACTION1ALLO2 - 68
24X-RAY DIFFRACTION1ALLO101
25X-RAY DIFFRACTION1ALLQ24 - 246
26X-RAY DIFFRACTION1ALLQ301 - 304
27X-RAY DIFFRACTION1ALLR2 - 68
28X-RAY DIFFRACTION1ALLR101
29X-RAY DIFFRACTION1ALLT24 - 246
30X-RAY DIFFRACTION1ALLT301 - 302
31X-RAY DIFFRACTION1ALLV2 - 68
32X-RAY DIFFRACTION1ALLV101 - 102

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