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- PDB-5fnw: Crystal structure at pH 7.0 of a potato STI-Kunitz bi-functional ... -

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Basic information

Entry
Database: PDB / ID: 5fnw
TitleCrystal structure at pH 7.0 of a potato STI-Kunitz bi-functional inhibitor of serine and aspartic proteases in space group p4322 and ph 9.0
ComponentsPOTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D
KeywordsHYDROLASE INHIBITOR / HYDROLASE / STI-KUNITZ INHIBITOR / ASPARTIC PROTEASES / SERINE PROTEASES / PROTEASE INHIBITOR / BI-FUNCTIONAL PROTEASE INHIBITOR / KUNITZ-TYPE INHIBITOR
Function / homology
Function and homology information


aspartic-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Aspartic protease inhibitor 5
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGuerra, Y. / Rudino-Pinera, E.
CitationJournal: J. Struct. Biol. / Year: 2016
Title: Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop?
Authors: Guerra, Y. / Valiente, P.A. / Pons, T. / Berry, C. / Rudino-Pinera, E.
History
DepositionNov 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D


Theoretical massNumber of molelcules
Total (without water)20,5281
Polymers20,5281
Non-polymers00
Water59433
1
A: POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D

A: POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D


Theoretical massNumber of molelcules
Total (without water)41,0552
Polymers41,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Buried area2330 Å2
ΔGint-21.1 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.220, 77.220, 94.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D


Mass: 20527.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE OF THE POTATO STI-KUNITZ BI- FUNCTIONAL INHIBITOR E3AD_N19D HAS NOT BEEN DEPOSITED AT UNIPROT NOR GENBANK. MUTANT N19D
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Variant: ESTIMA / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: M1AKE5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsWHEN POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D WAS SEQUENCED RESIDUES 19 AND 177 WERE N ...WHEN POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D WAS SEQUENCED RESIDUES 19 AND 177 WERE N AND E RESPECTIVELY. HOWEVER, ELECTRON DENSITY MAPS CLEARLY SUPPORTS A CHANGE IN POSITIONS 19 AND 177 TO D AND K RESPECTIVELY

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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: 3.43 Å3/Da / Density % sol: 64.09 % / Description: NONE
Crystal growpH: 7
Details: CRYSTAL WAS CRYSTALLIZED FROM 15% (W/V) PEG 20000, 0.1 M HEPES PH 7.0, 30 MM GLYCYL-GLYCYL-GLYCINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 24, 2015 / Details: MICROBEAM
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→19.5 Å / Num. obs: 10963 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 58.19 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.01
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 19.28 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TC2

3tc2


Resolution: 2.45→19.497 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 503 4.6 %
Rwork0.2086 --
obs0.211 10961 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→19.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 33 1460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011471
X-RAY DIFFRACTIONf_angle_d1.2051995
X-RAY DIFFRACTIONf_dihedral_angle_d14.139551
X-RAY DIFFRACTIONf_chiral_restr0.045227
X-RAY DIFFRACTIONf_plane_restr0.006259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-2.69620.35591160.31952560X-RAY DIFFRACTION100
2.6962-3.0850.3361350.28312560X-RAY DIFFRACTION100
3.085-3.88170.28441220.22942600X-RAY DIFFRACTION100
3.8817-19.49810.21791300.16392738X-RAY DIFFRACTION99

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