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- PDB-1oyv: Crystal structure of tomato inhibitor-II in a ternary complex wit... -

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Basic information

Entry
Database: PDB / ID: 1oyv
TitleCrystal structure of tomato inhibitor-II in a ternary complex with subtilisin Carlsberg
Components
  • Subtilisin Carlsberg
  • Wound-induced proteinase inhibitor-II
KeywordsHYDROLASE / serine proteinase inhibitor / ternary complex / multidomain inhibitor / potato II family
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Subtilisin Carlsberg-like catalytic domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain ...Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Subtilisin Carlsberg-like catalytic domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin Carlsberg / Wound-induced proteinase inhibitor 2
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
Solanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBarrette-Ng, I.H. / Ng, K.K. / Cherney, M.M. / Pearce, G. / Ryan, C.A. / James, M.N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural basis of inhibition revealed by a 1:2 complex of the two-headed tomato inhibitor-II and subtilisin Carlsberg
Authors: Barrette-Ng, I.H. / Ng, K.K. / Cherney, M.M. / Pearce, G. / Ryan, C.A. / James, M.N.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin Carlsberg
B: Subtilisin Carlsberg
I: Wound-induced proteinase inhibitor-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1615
Polymers68,0813
Non-polymers802
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-22 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.971, 55.099, 91.338
Angle α, β, γ (deg.)90.00, 119.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Subtilisin Carlsberg


Mass: 27306.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / Strain: Nagarse / References: UniProt: P00780, subtilisin
#2: Protein Wound-induced proteinase inhibitor-II


Mass: 13468.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: leaves of tomato plant / Source: (natural) Solanum lycopersicum (tomato) / Strain: Bonny Best / References: UniProt: P05119
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.55 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, sodium malonate, sodium citrate, ethylene glycol, ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %(w/v)PEG80001reservoir
2200 mMsodium malonate1reservoir
375 mMsodium citrate1reservoirpH6.0
410 %(w/v)ethylene glycol1reservoir
55 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 23099 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2173 / Rsym value: 0.473 / % possible all: 94.1
Reflection
*PLUS
Num. obs: 23099 / Num. measured all: 97405
Reflection shell
*PLUS
% possible obs: 94.1 % / Num. unique obs: 2173 / Num. measured obs: 7394

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCN

1scn


Resolution: 2.5→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2293 -random
Rwork0.214 ---
obs0.22 23099 98.3 %-
all-23099 --
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.602 Å20 Å2-9.702 Å2
2---1.289 Å20 Å2
3---2.891 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 2 128 4751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_mcbond_it1.8721.5
X-RAY DIFFRACTIONc_scbond_it2.7792
X-RAY DIFFRACTIONc_mcangle_it2.9332
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.399 217 -
Rwork0.321 --
obs-2173 94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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