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- PDB-6e5m: Crystallographic structure of the cyclic nonapeptide derived from... -

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Basic information

Entry
Database: PDB / ID: 6e5m
TitleCrystallographic structure of the cyclic nonapeptide derived from the BTCI inhibitor bound to beta-trypsin in space group P 32 2 1
Components
  • 9MER-PEPTIDE
  • Cationic trypsin
Keywordshydrolase/hydrolase inhibitor / Inhibitor Complex / BTCI / 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. ...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 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
Serine protease 1 / Horsegram inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Vigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 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
DepositionJul 20, 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)24,4384
Polymers24,3012
Non-polymers1362
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The assembly has been confirmed by inhibitory activity assays.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-25 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.696, 68.696, 74.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-625-

HOH

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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) / Organ: Pancreas / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS pH 8.5 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.23983 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 31, 2016
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23983 Å / Relative weight: 1
ReflectionResolution: 1.61→25.263 Å / Num. obs: 26036 / % possible obs: 97 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07003 / Rrim(I) all: 0.07902 / Net I/σ(I): 12.74
Reflection shellResolution: 1.612→1.67 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2423 / CC1/2: 0.671 / Rrim(I) all: 0.7345 / % possible all: 93

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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: 1.612→25.263 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1885 1984 7.62 %
Rwork0.1565 --
obs0.159 26036 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.612→25.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 6 233 1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031779
X-RAY DIFFRACTIONf_angle_d0.6412433
X-RAY DIFFRACTIONf_dihedral_angle_d10.0121097
X-RAY DIFFRACTIONf_chiral_restr0.05274
X-RAY DIFFRACTIONf_plane_restr0.004312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6121-1.65240.34671260.31171555X-RAY DIFFRACTION90
1.6524-1.69710.30181450.2881730X-RAY DIFFRACTION100
1.6971-1.7470.24981430.24251764X-RAY DIFFRACTION100
1.747-1.80340.24881440.21371728X-RAY DIFFRACTION100
1.8034-1.86780.23591440.20281740X-RAY DIFFRACTION100
1.8678-1.94260.1991390.18521735X-RAY DIFFRACTION100
1.9426-2.03090.20271420.191766X-RAY DIFFRACTION100
2.0309-2.13790.19781440.16641726X-RAY DIFFRACTION99
2.1379-2.27180.20351390.15721674X-RAY DIFFRACTION95
2.2718-2.44710.17041410.15051729X-RAY DIFFRACTION98
2.4471-2.69310.1831450.1471711X-RAY DIFFRACTION97
2.6931-3.08220.18841460.14581723X-RAY DIFFRACTION97
3.0822-3.8810.17461380.12851712X-RAY DIFFRACTION95
3.881-25.26650.14791480.1251759X-RAY DIFFRACTION93
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)
10.4657-0.21830.24080.67480.42311.4733-0.01780.00540.0398-0.0488-0.0335-0.0975-0.1864-0.02630.03890.2188-0.0742-0.020.149-0.00690.170452.9725169.7304-6.0765
20.1612-0.24670.91410.6211-1.5895.2201-0.1952-0.05270.16790.1556-0.0862-0.113-0.5246-0.13740.22880.3043-0.0537-0.04690.1522-0.03110.216855.4339177.5860.6966
30.6319-0.1417-0.14850.91120.07432.719-0.07850.02650.0756-0.03050.0179-0.0539-0.1486-0.07850.08510.232-0.0572-0.03330.1639-0.02510.209853.3861173.75090.0827
41.40230.0170.94232.55950.37715.2027-0.03720.0389-0.0107-0.14940.00970.0348-0.3907-0.38930.01080.2151-0.0032-0.02430.211-0.01620.216644.1104174.5787-6.6647
50.164-0.3466-0.09552.9563-0.06451.4255-0.08990.056-0.20990.0760.03040.11010.1722-0.18710.06830.2584-0.0906-0.01430.2103-0.00770.228847.3709154.9399-0.439
63.4542-2.56833.38916.0366-3.8867.0781-0.14970.22070.31440.0399-0.2607-0.7386-0.15610.67910.37290.22-0.08330.00270.263-0.01280.272366.4029165.0993-7.4095
70.72060.1476-0.17931.8905-0.77331.8632-0.0085-0.0486-0.09620.2588-0.0277-0.13880.2177-0.03330.0210.276-0.0788-0.04380.150700.2155.8655153.81657.7974
82.3685-1.0323-0.57292.1628-0.70132.53440.0772-0.0323-0.07620.0513-0.1275-0.20190.06020.0990.04290.2198-0.0614-0.05710.157-0.01930.201659.9095156.81361.5407
91.7584-0.6058-0.52421.859-0.03241.64840.009-0.07790.03460.13960.0055-0.09860.1477-0.0741-0.01010.2144-0.0844-0.02930.1476-0.01110.174354.1372159.04254.262
103.1062-1.66152.0852.9243-3.6464.5447-0.1151-0.23060.20540.43220.50890.0933-0.2058-0.593-0.36790.216-0.00390.01270.3656-0.03860.234638.661173.22547.6394
114.50781.96210.42784.2619-1.290460.0705-0.43350.28290.4116-0.0168-0.683-0.4410.5286-0.12350.279-0.0931-0.07570.2416-0.02890.312264.4063168.53066.4201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 196 )
9X-RAY DIFFRACTION9chain 'A' and (resid 197 through 234 )
10X-RAY DIFFRACTION10chain 'A' and (resid 235 through 245 )
11X-RAY DIFFRACTION11chain 'I' and (resid 1 through 9 )

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