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- PDB-7aon: Crystal structure of CI2 double mutant L49I,I57V -

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Basic information

Entry
Database: PDB / ID: 7aon
TitleCrystal structure of CI2 double mutant L49I,I57V
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPROTEIN BINDING / Protease inhibitor
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsOlsen, J.G. / Teilum, K. / Hamborg, L. / Roche, J.V.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF15OC0016360 Denmark
Citation
Journal: Commun Biol / Year: 2021
Title: Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli.
Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K.
#1: Journal: Biorxiv / Year: 2020
Title: Synergistic stabilization of a double mutant in CI2 from an in-cell library screen
Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K.
History
DepositionOct 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5844
Polymers7,3001
Non-polymers2843
Water1,06359
1
A: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)91,00648
Polymers87,59512
Non-polymers3,41136
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_575-x,-y+2,z1
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation6_665x-y+1,x+1,z1
crystal symmetry operation7_467y-1,x+1,-z+21
crystal symmetry operation8_677x-y+1,-y+2,-z+21
crystal symmetry operation9_557-x,-x+y,-z+21
crystal symmetry operation10_667-y+1,-x+1,-z+21
crystal symmetry operation11_457-x+y-1,y,-z+21
crystal symmetry operation12_577x,x-y+2,-z+21
Buried area27140 Å2
ΔGint-407 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.392, 68.392, 52.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A


Mass: 7299.596 Da / Num. of mol.: 1 / Mutation: L49I, I57V
Source method: isolated from a genetically manipulated source
Details: CI-2 double mutant L49I, I57V / Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01053
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: Beautiful thick hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 40 % (NH4)2SO4, 50 mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.262→59.229 Å / Num. obs: 15866 / % possible obs: 94.7 % / Redundancy: 36.03 % / CC1/2: 0.9995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.016 / Rrim(I) all: 0.094 / Net I/σ(I): 22.585
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.262-1.34534.092.667493897950.70340.4622.7080.563.42
3.914-59.22931.450.05798777930.99930.010.05837.2100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.44 Å59.23 Å
Translation5 Å59.23 Å

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AOK

7aok


Resolution: 1.3→52.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.12 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 791 5.1 %RANDOM
Rwork0.1624 ---
obs0.1651 14868 84.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 24.235 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.3→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 16 59 587
Biso mean--37.89 33.89 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02545
X-RAY DIFFRACTIONr_bond_other_d0.0020.02565
X-RAY DIFFRACTIONr_angle_refined_deg3.1432.018741
X-RAY DIFFRACTIONr_angle_other_deg1.3531304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.604567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.9272522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61515107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.76154
X-RAY DIFFRACTIONr_chiral_restr0.1920.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021578
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02102
X-RAY DIFFRACTIONr_rigid_bond_restr8.3113537
X-RAY DIFFRACTIONr_sphericity_free34.833515
X-RAY DIFFRACTIONr_sphericity_bonded19.7625572
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 21 -
Rwork0.366 403 -
all-424 -
obs--31.64 %

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