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- PDB-3m7q: Crystal structure of recombinant Kunitz Type serine protease Inhi... -

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Basic information

Entry
Database: PDB / ID: 3m7q
TitleCrystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Caribbean sea anemone stichodactyla helianthus in complex with bovine pancreatic trypsin
Components
  • Cationic trypsin
  • Kunitz-type proteinase inhibitor SHPI-1
KeywordsHydrolase/Hydrolase inhibitor / Trypsin-Inhibitor complex / Kunitz-type serine-protease inhibitor / Digestion / Disulfide bond / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / Nematocyst / Protease inhibitor / Serine protease inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


nematocyst / aspartic-type endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis ...nematocyst / aspartic-type endopeptidase inhibitor activity / 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
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / 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
PHOSPHATE ION / Serine protease 1 / PI-stichotoxin-She2a
Similarity search - Component
Biological speciesStichodactyla helianthus (sea anemone)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGarcia-Fernandez, R. / Redecke, L. / Pons, T. / Perbandt, M. / Gil, D. / Talavera, A. / Gonzalez, Y. / de los angeles Chavez, M. / Betzel, C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural insights into serine protease inhibition by a marine invertebrate BPTI Kunitz-type inhibitor.
Authors: Garcia-Fernandez, R. / Pons, T. / Perbandt, M. / Valiente, P.A. / Talavera, A. / Gonzalez-Gonzalez, Y. / Rehders, D. / Chavez, M.A. / Betzel, C. / Redecke, L.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Cationic trypsin
B: Kunitz-type proteinase inhibitor SHPI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1153
Polymers30,0202
Non-polymers951
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.279, 66.551, 70.937
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 / 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: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein Kunitz-type proteinase inhibitor SHPI-1


Mass: 6695.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / Production host: Pichia pastoris (fungus) / References: UniProt: P31713
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.5 Å
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30937 / Redundancy: 5.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 9 / % possible all: 97.8

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHI

1shi


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.759 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18847 1540 5 %RANDOM
Rwork0.15778 ---
obs0.15938 30937 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 5 526 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212233
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.9453043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1882582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.69156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021710
X-RAY DIFFRACTIONr_nbd_refined0.1690.21022
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2360
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.298
X-RAY DIFFRACTIONr_mcbond_it1.03321503
X-RAY DIFFRACTIONr_mcangle_it1.46932356
X-RAY DIFFRACTIONr_scbond_it1.3232844
X-RAY DIFFRACTIONr_scangle_it1.9943687
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 109 -
Rwork0.189 2067 -
obs--97.53 %

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