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- PDB-7a1h: Crystal structure of wild-type CI2 -

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Basic information

Entry
Database: PDB / ID: 7a1h
TitleCrystal structure of wild-type CI2
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
DepositionAug 13, 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)7,5063
Polymers7,3141
Non-polymers1922
Water54030
1
A: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)90,06936
Polymers87,76312
Non-polymers2,30624
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 area22740 Å2
ΔGint-419 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.266, 68.266, 52.605
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: 7313.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Description: Beautiful three dimensional crystals with clear hexagonal faces. Size of crystals ranging from a few micrometer to app. 1 mm. Become blue when soaked with "Izit".
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40 % (NH4)2SO4, 50 mM Tris-Hcl, pH 8.0. Protein concentration app 75 mg/mL.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.5406 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 9, 2019 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 6063 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→1.949 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 453 / CC1/2: 0.565 / Rpim(I) all: 0.332 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å13.56 Å
Translation1.9 Å13.56 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CI2

2ci2


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.733 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 290 4.8 %RANDOM
Rwork0.2029 ---
obs0.2053 5773 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 23.35 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å2-0 Å2
2---0.74 Å20 Å2
3---2.41 Å2
Refinement stepCycle: final / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 10 30 553
Biso mean--50.81 25.98 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02528
X-RAY DIFFRACTIONr_bond_other_d0.0030.02544
X-RAY DIFFRACTIONr_angle_refined_deg2.0732.018716
X-RAY DIFFRACTIONr_angle_other_deg1.02831254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.607563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.04524.76221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.012154
X-RAY DIFFRACTIONr_chiral_restr0.110.287
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0298
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 21 -
Rwork0.248 399 -
all-420 -
obs--99.76 %

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