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- PDB-6atw: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 6atw
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsChlorotoxin
KeywordsTOXIN / Knottins / Cystine knot / Toxins
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 / Resolution: 1.53 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
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
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)4,1561
Polymers4,1561
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.539, 26.312, 48.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Chlorotoxin / ClTx


Mass: 4155.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus quinquestriatus (Egyptian scorpion)
Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P45639
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.71 Å3/Da / Density % sol: 28.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M Na malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 7263 / % possible obs: 86.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.023 / Net I/σ(I): 13.1
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.126 / Num. unique obs: 46 / CC1/2: 0.935 / Rpim(I) all: 0.076 / % possible all: 10.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→24.02 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.065 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17821 196 4.8 %RANDOM
Rwork0.13348 ---
obs0.13555 3857 87.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.53→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms279 0 0 55 334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019299
X-RAY DIFFRACTIONr_bond_other_d0.0010.02272
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.985400
X-RAY DIFFRACTIONr_angle_other_deg0.7583638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.501541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.92321.81811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9451559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.27153
X-RAY DIFFRACTIONr_chiral_restr0.1150.237
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0266
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0960.781155
X-RAY DIFFRACTIONr_mcbond_other1.0810.779154
X-RAY DIFFRACTIONr_mcangle_it1.6241.747193
X-RAY DIFFRACTIONr_mcangle_other1.6271.75194
X-RAY DIFFRACTIONr_scbond_it2.4241.019144
X-RAY DIFFRACTIONr_scbond_other2.421.018144
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8782.157205
X-RAY DIFFRACTIONr_long_range_B_refined5.57116.871339
X-RAY DIFFRACTIONr_long_range_B_other5.18315.455324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.534→1.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 3 -
Rwork0.227 52 -
obs--16.82 %

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