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- PDB-3s8j: Crystal structure of a papaya latex serine protease inhibitor (PP... -

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Basic information

Entry
Database: PDB / ID: 3s8j
TitleCrystal structure of a papaya latex serine protease inhibitor (PPI) at 2.6A resolution
ComponentsLatex serine proteinase inhibitor
KeywordsHYDROLASE INHIBITOR / Kunitz-STI fold / serine protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
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
ACETATE ION / FORMIC ACID / Latex serine proteinase inhibitor
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarcia-Pino, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition
Authors: Azarkan, M. / Martinez-Rodriguez, S. / Buts, L. / Baeyens-Volant, D. / Garcia-Pino, A.
History
DepositionMay 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Latex serine proteinase inhibitor
B: Latex serine proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,28812
Polymers41,3662
Non-polymers92210
Water1,63991
1
A: Latex serine proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1015
Polymers20,6831
Non-polymers4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Latex serine proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1867
Polymers20,6831
Non-polymers5036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.699, 74.699, 78.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Latex serine proteinase inhibitor


Mass: 20682.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PPI was extracted from C. papaya latex / Source: (natural) Carica papaya (papaya) / References: UniProt: P80691
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 99 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.5 M sodium formate, 0.1 M sodium acetate, 0.1 M ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 4, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. all: 15065 / Num. obs: 15065 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.88 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 24.4
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→14.966 Å / σ(F): 1.98 / Phase error: 31.23 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2131 1251 8.3 %
Rwork0.1503 --
obs0.1532 15065 100 %
all-15065 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.944 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7594 Å20 Å20 Å2
2---2.7594 Å2-0 Å2
3---5.5188 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 60 91 2905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092901
X-RAY DIFFRACTIONf_angle_d1.2363957
X-RAY DIFFRACTIONf_dihedral_angle_d13.386994
X-RAY DIFFRACTIONf_chiral_restr0.081438
X-RAY DIFFRACTIONf_plane_restr0.006510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6236-2.7260.33642020.24191433X-RAY DIFFRACTION88
2.726-2.84660.33181280.2181459X-RAY DIFFRACTION92
2.8466-2.99190.24881300.18951485X-RAY DIFFRACTION92
2.9919-3.17220.21851280.17481460X-RAY DIFFRACTION92
3.1722-3.40570.23341260.16071488X-RAY DIFFRACTION92
3.4057-3.72780.19771280.14841491X-RAY DIFFRACTION92
3.7278-4.22150.2021300.1271455X-RAY DIFFRACTION92
4.2215-5.15960.18991140.11531483X-RAY DIFFRACTION93
5.1596-9.23790.18741650.13441444X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7866-0.12080.4741.1946-0.1522.3390.29110.1498-0.27560.0011-0.0748-0.07280.35420.074-0.11170.39580.02350.01430.16520.00310.4095-7.7992-16.9252-1.2804
23.1108-1.6531-1.43781.2171-0.28727.2274-0.164-1.37540.19641.55040.26690.13290.3773-0.6837-0.2980.6644-0.00710.02240.577-0.03170.3742-22.9944-10.327417.8529
32.643-1.2514-0.02061.97590.18892.4854-0.010.169-0.04480.0096-0.15070.0677-0.0971-0.37420.14590.26140.05760.00970.22790.00180.3259-15.1881-7.6334-0.3601
41.0404-0.4148-0.22481.9732-1.03111.8840.061-0.0857-0.05080.0704-0.1441-0.3498-0.1416-0.03590.09110.41570.0048-0.01070.2433-0.02090.4647-8.635-6.31377.0869
52.2991-0.5353-0.39081.7889-0.10332.24730.2046-0.13070.52430.2439-0.27150.0588-0.32690.12-0.01730.432-0.0644-0.02510.2260.00120.4361-11.3982-24.026731.0023
61.74850.2762-0.04893.8115-0.36181.7033-0.2320.00570.1815-0.8943-0.06650.0365-0.0369-0.43530.26460.61270.0407-0.09830.33020.06660.3928-21.4541-23.823718.2492
72.9797-0.0239-0.02923.44680.24173.9740.141-0.38090.23390.0088-0.29570.2003-0.2285-0.40280.18810.3784-0.0526-0.00760.30210.03270.3894-19.8599-28.708234.4176
80.68430.1888-0.73443.161-1.28561.6599-0.0282-0.0587-0.1052-0.3107-0.06780.02570.0595-0.12430.03350.3511-0.1183-0.00930.27810.00680.367-16.1586-35.450625.9604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:39)
2X-RAY DIFFRACTION2(chain A and resid 40:47)
3X-RAY DIFFRACTION3(chain A and resid 48:147)
4X-RAY DIFFRACTION4(chain A and resid 148:183)
5X-RAY DIFFRACTION5(chain B and resid 3:41)
6X-RAY DIFFRACTION6(chain B and resid 42:54)
7X-RAY DIFFRACTION7(chain B and resid 55:98)
8X-RAY DIFFRACTION8(chain B and resid 99:183)

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