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- PDB-2f3c: Crystal structure of infestin 1, a Kazal-type serineprotease inhi... -

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Basic information

Entry
Database: PDB / ID: 2f3c
TitleCrystal structure of infestin 1, a Kazal-type serineprotease inhibitor, in complex with trypsin
Components
  • Cationic trypsin
  • thrombin inhibitor infestin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease - inhibitor complex / Kazal-type domain / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
: / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...: / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / : / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Serine protease 1 / Thrombin inhibitor infestin
Similarity search - Component
Biological speciesTriatoma infestans (insect)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCampos, I.T.N. / Tanaka, A.S. / Barbosa, J.A.R.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The Kazal-type inhibitors infestins 1 and 4 differ in specificity but are similar in three-dimensional structure.
Authors: Campos, I.T. / Souza, T.A. / Torquato, R.J. / De Marco, R. / Tanaka-Azevedo, A.M. / Tanaka, A.S. / Barbosa, J.A.R.G.
History
DepositionNov 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Database references
Revision 1.4Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software
Revision 1.6Aug 23, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Cationic trypsin
I: thrombin inhibitor infestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8097
Polymers29,3852
Non-polymers4245
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-68 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.993, 62.692, 67.837
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


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: residues 21-243 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein thrombin inhibitor infestin


Mass: 6060.617 Da / Num. of mol.: 1 / Fragment: residues 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triatoma infestans (insect) / Plasmid: pIC 3.1.3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): H003 / References: GenBank: 14211145, UniProt: Q95P16*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2004
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.501→46.127 Å / Num. all: 8984 / Num. obs: 8955 / % possible obs: 99.7 % / Redundancy: 4.5 %
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / % possible all: 98.1

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Phasing

Phasing MRRfactor: 0.465 / Cor.coef. Fo:Fc: 0.446
Highest resolutionLowest resolution
Rotation5 Å36.06 Å
Translation5 Å36.06 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AN1 and 2ERW

1an1

2erw


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.879 / SU B: 19.125 / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.135 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SIMULATED ANNEALING WAS PERFORMED WITH THE CNS SOFTWARE IN THE FIRST CYCLE OF REFINEMENT. TLS APPLIED USING EACH PROTEIN MOLECULE AS AN INDIVIDUAL GROUP.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 424 4.7 %RANDOM
Rwork0.17 ---
all0.174 8948 --
obs-8948 99.71 %-
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: 26.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--1.01 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 21 91 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212008
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9572735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.76325.83372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.263153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021492
X-RAY DIFFRACTIONr_nbd_refined0.2120.21124
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2177
X-RAY DIFFRACTIONr_metal_ion_refined0.170.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.29
X-RAY DIFFRACTIONr_mcbond_it0.511.51339
X-RAY DIFFRACTIONr_mcangle_it0.93822112
X-RAY DIFFRACTIONr_scbond_it1.5353758
X-RAY DIFFRACTIONr_scangle_it2.3924.5623
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 36 -
Rwork0.241 589 -
obs-625 97.35 %

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