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- PDB-3ru4: Crystal structure of the Bowman-Birk serine protease inhibitor BT... -

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Basic information

Entry
Database: PDB / ID: 3ru4
TitleCrystal structure of the Bowman-Birk serine protease inhibitor BTCI in complex with trypsin and chymotrypsin
Components
  • (Chymotrypsinogen ...) x 3
  • Bowman-Birk type seed trypsin and chymotrypsin inhibitor
  • Cationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease and bowman-birk fold / digestion and inhibition / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chymotrypsin / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space ...chymotrypsin / 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
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / 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 / Chymotrypsinogen A / Bowman-Birk type seed trypsin and chymotrypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Vigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsEsteves, G.F. / Santos, C.R. / Ventura, M.M. / Barbosa, J.A.R.G. / Freitas, S.M.
Citation
Journal: To be Published
Title: Crystal structure of the Bowman-Birk serine protease inhibitor BTCI in complex with trypsin and chymotrypsin
Authors: Esteves, G.F. / Teles, R.C.L. / Cavalcante, N.S. / Neves, D. / Ventura, M.M. / Barbosa, J.A.R.G. / Freitas, S.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization, data collection and processing of the chymotrypsin-BTCI-trypsin ternary complex.
Authors: Esteves, G.F. / Teles, R.C. / Cavalcante, N.S. / Neves, D. / Ventura, M.M. / Barbosa, J.A. / de Freitas, S.M.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Cationic trypsin
B: Bowman-Birk type seed trypsin and chymotrypsin inhibitor
C: Chymotrypsinogen A
D: Chymotrypsinogen A
E: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,10129
Polymers55,0355
Non-polymers2,06624
Water12,502694
1
T: Cationic trypsin
hetero molecules

B: Bowman-Birk type seed trypsin and chymotrypsin inhibitor
C: Chymotrypsinogen A
D: Chymotrypsinogen A
E: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,10129
Polymers55,0355
Non-polymers2,06624
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-196 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.477, 54.571, 69.286
Angle α, β, γ (deg.)67.28, 71.04, 73.55
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 2 molecules TB

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


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 Bowman-Birk type seed trypsin and chymotrypsin inhibitor / BTCI


Mass: 6689.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna unguiculata (cowpea) / References: UniProt: P17734

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Chymotrypsinogen ... , 3 types, 3 molecules CDE

#3: Protein/peptide Chymotrypsinogen A / Chymotrypsin A chain A


Mass: 1083.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein Chymotrypsinogen A / Chymotrypsin A chain B


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#5: Protein Chymotrypsinogen A / Chymotrypsin A chain C


Mass: 10003.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin

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Non-polymers , 6 types, 718 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol (PEG) 6000, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2007 / Details: mirrors
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.675→62.02 Å / Num. all: 57400 / Num. obs: 57400 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.87
Reflection shellResolution: 1.675→1.74 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.28 / % possible all: 27.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2G81 AND 4CHA

2g81

4cha


Resolution: 1.68→62.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.735 / SU ML: 0.068 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19249 2899 5.1 %RANDOM
Rwork0.1572 ---
obs0.15901 54466 80.22 %-
all-54466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0.06 Å21.17 Å2
2---0.76 Å20.57 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.68→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 122 694 4650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224125
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.241.9675628
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02625.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.568159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.52637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60524270
X-RAY DIFFRACTIONr_scbond_it2.83331488
X-RAY DIFFRACTIONr_scangle_it3.8794.51340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.675→1.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.628 51 -
Rwork0.547 1123 -
obs--22.16 %
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)
11.5307-0.2399-0.43052.6084-0.20882.1695-0.0186-0.0122-0.02210.1031-0.00510.01380.08670.02380.02370.0104-0.0042-0.00680.024-0.00470.0247-14.865-11.903311.2033
23.04722.6554-3.03462.3974-2.57073.57380.2027-0.25420.10380.2183-0.1650.0051-0.17690.1887-0.03770.0631-0.0114-0.03280.0975-0.03330.10181.78268.066211.2856
31.74620.1457-0.23142.0303-0.68683.07620.00330.08880.0026-0.156-0.0096-0.0492-0.0035-0.03560.00630.01170.0061-0.00060.0311-0.0140.024714.13910.463-12.8393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T16 - 238
2X-RAY DIFFRACTION2B14 - 74
3X-RAY DIFFRACTION3C1 - 11
4X-RAY DIFFRACTION3D16 - 146
5X-RAY DIFFRACTION3E150 - 245

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