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- PDB-5dvh: Structure of the Kunitz-type cysteine protease inhibitor PCPI-3 f... -

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Basic information

Entry
Database: PDB / ID: 5dvh
TitleStructure of the Kunitz-type cysteine protease inhibitor PCPI-3 from potato
ComponentsPCPI-3
Keywordsprotease inhibitor / Plant Kunitz-family inhibitor
Function / homology
Function and homology information


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
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBrynda, J. / Mishra, M. / Mares, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation15-18929S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicInterBioMed LO1302 Czech Republic
Czech Academy of SciencesRVO61388963 Czech Republic
CitationJournal: To Be Published
Title: Structure of the Kunitz-type cysteine protease inhibitor PCPI-3 from potato
Authors: Brynda, J. / Mishra, M. / Mares, M.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PCPI-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4184
Polymers21,3121
Non-polymers1063
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-21 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.637, 76.637, 107.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PCPI-3


Mass: 21312.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / Variant: Karin cultivar / References: UniProt: A0A1I9GEQ4*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Reservoir: 3 M sodium chloride, 0.1 M sodium acetate pH 5.5 Protein buffer and concentration: 5 mM sodium acetate pH 5.5 Protein concentration = 10 mg/ml protein:reservoir = 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→48.37 Å / Num. obs: 30248 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 32.094 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.49
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.911.3331.36198
1.91-2.040.783.091100
2.04-2.20.4365.451100
2.2-2.410.2728.491100
2.41-2.70.17712.291100
2.7-3.110.09321.141100
3.11-3.810.05234.811100
3.81-5.370.03945.951100
5.370.03545.35199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation48.37 Å3.5 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1755 / FOM work R set: 0.862 / SU B: 2.15 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0976 / SU Rfree: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1513 5 %RANDOM
Rwork0.1972 ---
obs0.1985 28731 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.12 Å2 / Biso mean: 23.368 Å2 / Biso min: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 1.8→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 3 157 1599
Biso mean--29.67 32.88 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021509
X-RAY DIFFRACTIONr_bond_other_d0.0030.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9622059
X-RAY DIFFRACTIONr_angle_other_deg0.8613.0052516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9824.53164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9515238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.467154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 93 -
Rwork0.36 1839 -
all-1932 -
obs--95.5 %

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