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- PDB-5fnx: Crystal structure at pH 9.0 of a potato STI-Kunitz bi-functional ... -

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Basic information

Entry
Database: PDB / ID: 5fnx
TitleCrystal structure at pH 9.0 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 / negative regulation of peptidase 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: 2.65 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 23, 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
Water34219
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 area2340 Å2
ΔGint-19.2 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.940, 77.940, 95.010
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.
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.: 19 / 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: 3.52 Å3/Da / Density % sol: 65.03 % / Description: NONE
Crystal growpH: 9
Details: CRYSTAL WAS CRYSTALLIZED FROM 10% MPD, 0.1M BICINE PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / 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: 2.65→19.5 Å / Num. obs: 8941 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Biso Wilson estimate: 72.42 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.61
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 19.24 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 5.98 / % 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: 2.65→19.451 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 391 4.4 %
Rwork0.208 --
obs0.2104 8936 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 19 1446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121470
X-RAY DIFFRACTIONf_angle_d1.51995
X-RAY DIFFRACTIONf_dihedral_angle_d15.525549
X-RAY DIFFRACTIONf_chiral_restr0.06227
X-RAY DIFFRACTIONf_plane_restr0.008260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.03230.35661260.30372777X-RAY DIFFRACTION100
3.0323-3.81560.30821350.25392813X-RAY DIFFRACTION100
3.8156-19.45120.22291300.17282955X-RAY DIFFRACTION99

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