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- PDB-5g00: CRYSTAL STRUCTURE OF A POTATO STI-KUNITZ BIFUNCTIONAL INHIBITOR O... -

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Basic information

Entry
Database: PDB / ID: 5g00
TitleCRYSTAL STRUCTURE OF A POTATO STI-KUNITZ BIFUNCTIONAL INHIBITOR OF SERINE AND ASPARTIC PROTEASES IN SPACE GROUP P4322 AND PH 7.4
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


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: 2.5 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 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KTI-A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7482
Polymers20,5271
Non-polymers2211
Water34219
1
A: KTI-A PROTEIN
hetero molecules

A: KTI-A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4954
Polymers41,0532
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Buried area2740 Å2
ΔGint-11.5 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 77.180, 95.900
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 KTI-A PROTEIN


Mass: 20526.504 Da / Num. of mol.: 1 / Fragment: HYDROLASE INHIBITOR
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.52 %
Description: DATA WAS ANISOTROPICALLY CORRECTED WITH THE WEBSERVER DIFFRACTION ANISOTROPY SERVER UCLA
Crystal growpH: 7.4
Details: 10% (W/V) PEG 2000 MME, 0.1 M TRIS-HCL PH 8.5, 0.2 M TRIMETHYLAMINE N-OXIDE, 30 MM GLYCYL-GLYCL-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: 2.5→29.5 Å / Num. obs: 10356 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Biso Wilson estimate: 60.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.82
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 16.63 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.89 / % possible all: 74.1

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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: 2.5→36.021 Å / SU ML: 0.27 / σ(F): 1.37 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 499 4.8 %
Rwork0.228 --
obs0.2288 10329 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 14 19 1460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011475
X-RAY DIFFRACTIONf_angle_d1.3452001
X-RAY DIFFRACTIONf_dihedral_angle_d14.417545
X-RAY DIFFRACTIONf_chiral_restr0.05230
X-RAY DIFFRACTIONf_plane_restr0.007259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75160.32821030.31752262X-RAY DIFFRACTION92
2.7516-3.14960.33111430.30312429X-RAY DIFFRACTION100
3.1496-3.96730.2991280.25652499X-RAY DIFFRACTION100
3.9673-36.02520.18421250.18432640X-RAY DIFFRACTION100

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