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- PDB-4hgc: Crystal structure of bovine trypsin complexed with sfti-1 analog ... -

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Basic information

Entry
Database: PDB / ID: 4hgc
TitleCrystal structure of bovine trypsin complexed with sfti-1 analog containing a peptoid residue at position p1
Components
  • Cationic trypsin
  • Trypsin inhibitor 1
KeywordsHydrolase/Hydrolase Inhibitor / HYDROLASE / SERINE PROTEASE / CYCLIC PEPTIDE / PEPTOID / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity ...negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / 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 / Trypsin-like serine proteases ...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
Trypsin inhibitor 1 / Serine protease 1 / Trypsin inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsKrzywda, S. / Jaskolski, M. / Rolka, K. / Stawikowski, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of a proteolytically resistant analogue of (NLys)(5)SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis.
Authors: Krzywda, S. / Jaskolski, M. / Rolka, K. / Stawikowski, M.J.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _diffrn_source.pdbx_synchrotron_site / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
I: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,64811
Polymers24,8592
Non-polymers7899
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-52 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.12, 64.14, 70.04
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

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


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: unp residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Type: Oligopeptide / Class: Inhibitor / Mass: 1534.822 Da / Num. of mol.: 1 / Fragment: unp residues 40-53 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1

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Non-polymers , 4 types, 296 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 M ammonium sulphate, 1 mM benzamidine and 0.1 M Mes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2007 / Details: mirrors
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.29→37.17 Å / Num. all: 67689 / Num. obs: 67689 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.5
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2 / Num. unique all: 9680 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFI

1sfi


Resolution: 1.29→30.74 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.331 / SU ML: 0.025 / Isotropic thermal model: anisotropic / Cross valid method: R-free / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinement. Hydrogen atoms were added at riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 2036 3 %RANDOM
Rwork0.12623 ---
obs0.12714 65592 99.2 %-
all-65592 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.878 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.29→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 46 287 2052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021817
X-RAY DIFFRACTIONr_bond_other_d0.0070.021214
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9682442
X-RAY DIFFRACTIONr_angle_other_deg2.0983.0112970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7385225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01425.62564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61715286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.989153
X-RAY DIFFRACTIONr_chiral_restr0.130.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02317
X-RAY DIFFRACTIONr_rigid_bond_restr4.97733031
X-RAY DIFFRACTIONr_sphericity_free29.3715105
X-RAY DIFFRACTIONr_sphericity_bonded14.59153192
LS refinement shellResolution: 1.29→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 136 -
Rwork0.256 4475 -
obs-4475 98.29 %

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