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- PDB-7a3m: Synergistic stabilization of a double mutant in CI2 from an in-ce... -

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Basic information

Entry
Database: PDB / ID: 7a3m
TitleSynergistic stabilization of a double mutant in CI2 from an in-cell library screen
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPROTEIN BINDING / Chymotrypsin inhibitor CI-2 / mutant
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: 1.01 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 18, 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


Theoretical massNumber of molelcules
Total (without water)7,3001
Polymers7,3001
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.435, 68.435, 52.104
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: I57V
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 47 % / Description: Beautiful, thick hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: 1.006→59.27 Å / Num. obs: 29926 / % possible obs: 95.4 % / Redundancy: 32.4 % / CC1/2: 1 / Rpim(I) all: 0.015 / Net I/σ(I): 22.9
Reflection shellResolution: 1.006→1.069 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1496 / CC1/2: 0.498 / Rpim(I) all: 0.506 / % possible all: 60.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACv5.5refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERv2.5.5phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A2E

7a2e
PDB Unreleased entry


Resolution: 1.01→59.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.789 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1426 4.8 %RANDOM
Rwork0.1489 ---
obs0.1504 28501 77.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.71 Å2 / Biso mean: 14.761 Å2 / Biso min: 6.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.01→59.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 98 610
Biso mean---23.82 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.019536
X-RAY DIFFRACTIONr_bond_other_d0.0020.02563
X-RAY DIFFRACTIONr_angle_refined_deg2.5161.997729
X-RAY DIFFRACTIONr_angle_other_deg1.34831297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96924.09122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50715107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.654155
X-RAY DIFFRACTIONr_chiral_restr0.140.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021584
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02105
X-RAY DIFFRACTIONr_rigid_bond_restr6.57431099
X-RAY DIFFRACTIONr_sphericity_free27.006516
X-RAY DIFFRACTIONr_sphericity_bonded9.98951172
LS refinement shellResolution: 1.01→1.032 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.345 15 -
Rwork0.348 230 -
obs--8.77 %

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