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- PDB-5fzy: CRYSTAL STRUCTURE OF N19D POTATO STI-KUNITZ BI-FUNCTIONAL INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 5fzy
TitleCRYSTAL STRUCTURE OF N19D POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR OF SERINE AND ASPARTIC PROTEASES IN SPACE GROUP C2221 AND PH 3.5
ComponentsKTI-A PROTEIN
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


serine-type endopeptidase inhibitor activity / peptidase activity / proteolysis
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
KTI-A protein / Aspartic protease inhibitor 5
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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
DepositionMar 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KTI-A PROTEIN
B: KTI-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0552
Polymers41,0552
Non-polymers00
Water93752
1
A: KTI-A PROTEIN

A: KTI-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0552
Polymers41,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2230 Å2
ΔGint-20.6 kcal/mol
Surface area17690 Å2
MethodPISA
2
B: KTI-A PROTEIN

B: KTI-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0552
Polymers41,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2250 Å2
ΔGint-20.1 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.950, 114.240, 98.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2011-

HOH

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Components

#1: Protein KTI-A PROTEIN


Mass: 20527.490 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Variant: ESTIMA / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: A0A097H118, UniProt: M1AKE5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS DEPOSIT HAS A MUTATION IN RESIDUE 19 FROM N TO D.

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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: 3.54 Å3/Da / Density % sol: 65.24 % / Description: NONE
Crystal growpH: 3.5
Details: 20% (W/V) PEG 8000, 0.1 M HEPES PH 7.5, 0.1 M GLYCINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1807
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2016 / Details: SI (111) DOUBLE CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 2.47→38.42 Å / Num. obs: 21238 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.59 % / Biso Wilson estimate: 60.57 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.06
Reflection shellResolution: 2.47→2.57 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.24 / % 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 5FNW

5fnw


Resolution: 2.47→19.897 Å / SU ML: 0.59 / σ(F): 1.35 / Phase error: 37.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1035 4.9 %
Rwork0.2253 --
obs0.2277 21184 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.1 Å2
Refinement stepCycle: LAST / Resolution: 2.47→19.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 52 2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012922
X-RAY DIFFRACTIONf_angle_d1.3883964
X-RAY DIFFRACTIONf_dihedral_angle_d15.7581088
X-RAY DIFFRACTIONf_chiral_restr0.048452
X-RAY DIFFRACTIONf_plane_restr0.006516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.60.45371550.41532832X-RAY DIFFRACTION100
2.6-2.76250.43051400.37562832X-RAY DIFFRACTION100
2.7625-2.97510.40771550.352845X-RAY DIFFRACTION100
2.9751-3.27330.41311510.32882850X-RAY DIFFRACTION100
3.2733-3.74420.35721410.26212882X-RAY DIFFRACTION100
3.7442-4.7070.22941530.18132904X-RAY DIFFRACTION100
4.707-19.89770.16311400.14333004X-RAY DIFFRACTION100

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