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- PDB-3gy3: A comparative study on the inhibition of bovine beta-trypsin by b... -

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Basic information

Entry
Database: PDB / ID: 3gy3
TitleA comparative study on the inhibition of bovine beta-trypsin by bis-benzamidines diminazene and pentamidine by X-ray crystallography and ITC
ComponentsCationic trypsin
KeywordsHYDROLASE / bovine beta-trypsin / pentamidine / protein-ligand complex / protein-ligand interaction / Calcium / Digestion / Disulfide bond / Metal-binding / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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
1,5-BIS(4-AMIDINOPHENOXY)PENTANE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPerilo, C.S. / Pereira, M.T. / Santoro, M.M. / Nagem, R.A.P.
CitationJournal: Int.J.Biol.Macromol. / Year: 2010
Title: Structural binding evidence of the trypanocidal drugs Berenil and Pentacarinate active principles to a serine protease model.
Authors: Perilo, C.S. / Pereira, M.T. / Santoro, M.M. / Nagem, R.A.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_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

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,13910
Polymers23,3241
Non-polymers8159
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.393, 53.393, 104.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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 / Details: pancreatic / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O2 / Comment: medication, Antimicrobial*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14.5% PEG4000, 0.1M ammonium sulfate, 0.05M Tris-HCl, 0.008M CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.428 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 27, 2006 / Details: mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.428 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 20068 / Num. obs: 19849 / % possible obs: 98.91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rsym value: 0.042 / Net I/σ(I): 55.5
Reflection shellResolution: 1.7→1.739 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 1753 / Rsym value: 0.201 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.249 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21184 1013 5.1 %RANDOM
Rwork0.17534 ---
obs0.17721 18796 99.78 %-
all-19853 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 54 213 1896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221739
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9692343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85125.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.03152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021261
X-RAY DIFFRACTIONr_nbd_refined0.2660.21236
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2296
X-RAY DIFFRACTIONr_metal_ion_refined0.150.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.227
X-RAY DIFFRACTIONr_mcbond_it0.91.51120
X-RAY DIFFRACTIONr_mcangle_it1.35221777
X-RAY DIFFRACTIONr_scbond_it2.4383689
X-RAY DIFFRACTIONr_scangle_it3.2344.5562
LS refinement shellResolution: 1.7→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 84 -
Rwork0.269 1338 -
obs--97.2 %

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