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- PDB-6eat: Crystallographic structure of the cyclic nonapeptide derived from... -

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Basic information

Entry
Database: PDB / ID: 6eat
TitleCrystallographic structure of the cyclic nonapeptide derived from the BTCI inhibitor bound to beta-trypsin in space group P 21 21 21.
Components
  • 9MER-PEPTIDE
  • Cationic trypsin
Keywordshydrolase/hydrolase inhibitor / Inhibitor Complex / BTCI / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / 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. ...Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / 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 / 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
Serine protease 1 / Horsegram inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Vigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.149 Å
AuthorsFernandes, J.C. / Valadares, N.F. / Freitas, S.M. / Barbosa, J.A.R.G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)309054/2014-1 Brazil
CitationJournal: Arch. Biochem. Biophys. / Year: 2019
Title: Crystallographic structure of a complex between trypsin and a nonapeptide derived from a Bowman-Birk inhibitor found in Vigna unguiculata seeds.
Authors: Fernandes, J.P.C. / Mehdad, A. / Valadares, N.F. / Mourao, C.B.F. / Ventura, M.M. / Barbosa, J.A.R.G. / Freitas, S.M.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
I: 9MER-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49415
Polymers24,3012
Non-polymers1,19313
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The assembly has been confirmed by enzymatic activity assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-162 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.834, 61.569, 67.030
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 (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide 9MER-PEPTIDE


Mass: 977.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vigna unguiculata (cowpea) / References: UniProt: Q9S9E3*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes sodium 1 M Monohydrate lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.20011 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 31, 2018
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.20011 Å / Relative weight: 1
ReflectionResolution: 1.149→29.917 Å / Num. obs: 83153 / % possible obs: 94 % / Redundancy: 14 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 1 / Net I/σ(I): 30.21
Reflection shellResolution: 1.149→1.19 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 6078 / CC1/2: 0.651 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RU4

3ru4


Resolution: 1.149→29.917 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.05
RfactorNum. reflection% reflection
Rfree0.1545 2002 2.41 %
Rwork0.1439 --
obs0.1441 83128 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.149→29.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 61 369 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241876
X-RAY DIFFRACTIONf_angle_d1.4532580
X-RAY DIFFRACTIONf_dihedral_angle_d12.59696
X-RAY DIFFRACTIONf_chiral_restr0.091283
X-RAY DIFFRACTIONf_plane_restr0.008323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1493-1.17810.4808900.46063932X-RAY DIFFRACTION64
1.1781-1.20990.29541270.27275090X-RAY DIFFRACTION83
1.2099-1.24550.23261290.21935176X-RAY DIFFRACTION85
1.2455-1.28570.23451370.23095495X-RAY DIFFRACTION90
1.2857-1.33170.16611350.16225695X-RAY DIFFRACTION93
1.3317-1.3850.17761550.15536003X-RAY DIFFRACTION98
1.385-1.4480.15671470.14486113X-RAY DIFFRACTION99
1.448-1.52440.15791500.1416133X-RAY DIFFRACTION100
1.5244-1.61990.15181590.13666152X-RAY DIFFRACTION100
1.6199-1.74490.13721470.13646142X-RAY DIFFRACTION100
1.7449-1.92050.16031540.13256223X-RAY DIFFRACTION100
1.9205-2.19830.13451540.12826201X-RAY DIFFRACTION100
2.1983-2.76930.14931580.13196264X-RAY DIFFRACTION100
2.7693-29.92710.13671600.13396507X-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)
10.7878-0.2751-0.30791.25390.15311.13760.0091-0.0380.03430.06770.03610.0571-0.01820.0039-0.0450.0938-0.00030.00690.09870.00140.10335.096667.6534148.2681
21.4056-1.6736-0.38595.18090.00721.6435-0.0764-0.00490.03660.0510.04980.03130.117-0.05080.0330.0407-0.0297-0.00940.0847-0.00190.08811.057859.8883144.7556
30.8516-0.1857-0.81031.38660.32031.8434-0.04280.0001-0.0205-0.05180.0346-0.07570.18070.1556-0.00540.09220.01490.01220.09950.00340.080414.892560.2557136.2183
46.75330.9678-1.9151.0508-0.45642.0603-0.17390.07-0.124-0.11790.12620.01770.28840.0130.04890.13740.0073-0.00390.05350.00170.07376.458554.752138.5186
58.4548-0.67282.0476.1045-4.01125.8413-0.0103-0.301-0.14060.2276-0.2477-0.3170.25780.77130.21860.13840.0379-0.00960.18830.01950.096416.736756.3181149.8307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 245 )
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 9 )

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