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- PDB-5fzz: CRYSTAL STRUCTURE OF POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR OF... -

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Basic information

Entry
Database: PDB / ID: 5fzz
TitleCRYSTAL STRUCTURE OF POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR OF SERINE AND ASPARTIC PROTEASES IN SPACE GROUP P22121 AND PH 7.0
ComponentsKTI-A PROTEIN
KeywordsHYDROLASE / STI-KUNITZ INHIBITOR / ASPARTIC PROTEASES / SERINE PROTEASES / PROTEASE INHIBITOR / BI-FUNCTIONAL PROTEASE INHIBITOR / HYDROLASE 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
KTI-A protein / Aspartic protease inhibitor 5
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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

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Assembly

Deposited unit
A: KTI-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,5271
Polymers20,5271
Non-polymers00
Water1,02757
1
A: KTI-A PROTEIN

A: KTI-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0532
Polymers41,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_577x,-y+2,-z+21
Buried area2400 Å2
ΔGint-19.5 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.580, 56.450, 72.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein KTI-A PROTEIN


Mass: 20526.504 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.07 Å3/Da / Density % sol: 40.67 % / Description: NONE
Crystal growpH: 7
Details: 20% (W/V) PEG 3350, 0.1 M TRIS-HCL PH 7.0, 0.2 M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1807
DetectorType: MARRESEARCH MARMOSAIC / 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: 2.55→22.6 Å / Num. obs: 6643 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 7.73 % / Biso Wilson estimate: 33.56 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.69
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 8.12 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.08 / % possible all: 75.8

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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: 2.55→39.787 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.7 / Stereochemistry target values: ML
Details: DATA WAS ANISOTROPICALLY SCALED USING THE WEB SERVER DIFFRACTION ANISOTROPY SERVER (HTTP://SERVICES.MBI.UCLA.EDU/ANISOSCALE/)
RfactorNum. reflection% reflection
Rfree0.246 312 4.7 %
Rwork0.1814 --
obs0.1843 6619 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 2.55→39.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 57 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091473
X-RAY DIFFRACTIONf_angle_d1.1631999
X-RAY DIFFRACTIONf_dihedral_angle_d14.456551
X-RAY DIFFRACTIONf_chiral_restr0.041227
X-RAY DIFFRACTIONf_plane_restr0.005261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-3.21260.32851450.22873028X-RAY DIFFRACTION96
3.2126-39.79180.21141670.16163279X-RAY DIFFRACTION100

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