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- PDB-1pju: Unbound form of Tomato Inhibitor-II -

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Basic information

Entry
Database: PDB / ID: 1pju
TitleUnbound form of Tomato Inhibitor-II
ComponentsWound-induced proteinase inhibitor II
KeywordsHYDROLASE / Proteinase inhibitor
Function / homologyProteinase inhibitor I20 / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / serine-type endopeptidase inhibitor activity / 2-Layer Sandwich / extracellular region / Alpha Beta / Wound-induced proteinase inhibitor 2
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBarrette-Ng, I.H. / Ng, K.K.-S. / Cherney, M.M. / Pearce, G. / Ghani, U. / Ryan, C.A. / James, M.N.G.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Unbound form of tomato inhibitor-II reveals interdomain flexibility and conformational variability in the reactive site loops
Authors: Barrette-Ng, I.H. / Ng, K.K.-S. / Cherney, M.M. / Pearce, G. / Ghani, U. / Ryan, C.A. / James, M.N.G.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wound-induced proteinase inhibitor II
B: Wound-induced proteinase inhibitor II
C: Wound-induced proteinase inhibitor II
D: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,64212
Polymers53,8734
Non-polymers7698
Water3,153175
1
A: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6603
Polymers13,4681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6603
Polymers13,4681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6603
Polymers13,4681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6603
Polymers13,4681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Wound-induced proteinase inhibitor II
D: Wound-induced proteinase inhibitor II
hetero molecules

B: Wound-induced proteinase inhibitor II
D: Wound-induced proteinase inhibitor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,64212
Polymers53,8734
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6050 Å2
ΔGint-144 kcal/mol
Surface area23890 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.688, 106.607, 81.804
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe protein is likely a monomer in solution.

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Components

#1: Protein
Wound-induced proteinase inhibitor II


Mass: 13468.334 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / Strain: Bonny Best / References: UniProt: P05119
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 10K, Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 %(w/v)PEG100001reservoir
250 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2002 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 26506 / Num. obs: 26506 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 16.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2619 / Rsym value: 0.304 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 96074
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 2619 / Num. measured obs: 7412

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYV

1oyv


Resolution: 2.15→39.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.557 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.264 / ESU R Free: 0.208 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24983 1291 4.9 %RANDOM
Rwork0.20571 ---
all0.20786 25214 --
obs0.20786 25214 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å21 Å2
2--0.8 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 40 175 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213588
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9914860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435452
X-RAY DIFFRACTIONr_chiral_restr0.0750.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022812
X-RAY DIFFRACTIONr_nbd_refined0.1920.21475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.217
X-RAY DIFFRACTIONr_mcbond_it0.3241.52256
X-RAY DIFFRACTIONr_mcangle_it0.61823609
X-RAY DIFFRACTIONr_scbond_it1.08431332
X-RAY DIFFRACTIONr_scangle_it1.7424.51251
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 73
Rwork0.215 1866
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)
12.27060.052-0.4359.4022-1.00065.97120.09340.02250.11610.0286-0.0023-0.8453-0.3397-0.0248-0.09110.1191-0.04420.02150.0730.00470.211739.12380.360431.6389
23.1580.4944-2.01723.8233-0.12113.5213-0.1667-0.0496-0.2494-0.2624-0.0076-0.3480.25670.35740.17430.01930.01340.01410.15610.00110.141337.0174-20.307928.5429
33.91210.4517-0.69556.8743-0.55437.8488-0.1547-0.0949-0.1917-0.82540.28030.34730.7554-0.4013-0.12560.5455-0.14940.00940.22060.02490.23742.1813-27.1903-9.4067
42.8791-0.1757-0.35024.136-1.33749.3829-0.2054-0.26890.0874-0.06840.28160.2312-0.277-0.7116-0.07620.1145-0.0101-0.03730.236-0.01990.100146.5937-6.5474-11.1623
55.11550.94730.79239.2335-1.12385.11580.05510.0006-0.29070.3484-0.1043-0.29580.44760.44690.04930.1570.0542-0.06410.10020.03380.204533.9682-30.772748.3239
63.35541.15771.30433.59281.02454.57320.1583-0.13030.00350.2893-0.129-0.1817-0.22280.0972-0.02930.0363-0.0261-0.04110.07730.00940.075927.6397-10.06248.4192
75.74550.0293-0.88676.45471.23968.54660.35360.08540.36260.53530.01360.4883-1.1826-0.6952-0.36710.48420.19380.11740.28140.02930.258741.47034.29617.9938
83.81730.2549-3.56223.0255-1.96456.1342-0.30490.2145-0.20740.06240.08690.2640.3802-0.28570.21790.17540.04520.02840.3209-0.01720.157245.2541-16.777910.5587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 162 - 16
2X-RAY DIFFRACTION1AA76 - 11676 - 116
3X-RAY DIFFRACTION2AA17 - 7517 - 75
4X-RAY DIFFRACTION3BB3 - 163 - 16
5X-RAY DIFFRACTION3BB76 - 11576 - 115
6X-RAY DIFFRACTION4BB17 - 7517 - 75
7X-RAY DIFFRACTION5CC2 - 162 - 16
8X-RAY DIFFRACTION5CC76 - 11576 - 115
9X-RAY DIFFRACTION6CC17 - 7517 - 75
10X-RAY DIFFRACTION7DD2 - 162 - 16
11X-RAY DIFFRACTION7DD76 - 11576 - 115
12X-RAY DIFFRACTION8DD17 - 7517 - 75
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12
LS refinement shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.23 Å / Rfactor Rfree: 0.399 / Rfactor Rwork: 0.321

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