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- PDB-7soh: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 7soh
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsChlorotoxin
KeywordsTOXIN / CDP / Chlorotoxin
Function / homologyScorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily profile. / peptidase inhibitor activity / Knottin, scorpion toxin-like superfamily / chloride channel regulator activity / toxin activity / extracellular region / Chlorotoxin
Function and homology information
Biological speciesLeiurus quinquestriatus quinquestriatus (Egyptian scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsGewe, M.M. / Strong, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides.
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionOct 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorotoxin


Theoretical massNumber of molelcules
Total (without water)4,2401
Polymers4,2401
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.498, 26.350, 47.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Chlorotoxin / CTX / ClTx


Mass: 4239.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus quinquestriatus (Egyptian scorpion)
Production host: Homo sapiens (human) / References: UniProt: P45639
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.67 Å3/Da / Density % sol: 26.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M tri-Potassium Citrate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 2451 / % possible obs: 86 % / Redundancy: 5.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.064 / Net I/σ(I): 33
Reflection shellResolution: 1.81→1.875 Å / Num. unique obs: 91 / CC1/2: 0.95 / % possible all: 15.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ATW

6atw


Resolution: 1.81→23.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.172 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 114 4.6 %RANDOM
Rwork0.1734 ---
obs0.175 2339 85.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 34.08 Å2 / Biso mean: 13.514 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.9 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.81→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms276 0 0 15 291
Biso mean---14.63 -
Num. residues----38
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019284
X-RAY DIFFRACTIONr_bond_other_d0.0080.02242
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.965380
X-RAY DIFFRACTIONr_angle_other_deg1.1663560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.129537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1120.83312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7081547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.127154
X-RAY DIFFRACTIONr_chiral_restr0.1180.235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0268
LS refinement shellResolution: 1.81→1.853 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.34 3 -
Rwork0.235 44 -
obs--22.38 %

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