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

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Basic information

Entry
Database: PDB / ID: 6avd
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin alpha-KTx 6.9
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homology
Function and homology information


ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium channel toxin alpha-KTx 6.9
Similarity search - Component
Biological speciesOpistophthalmus carinatus (scorpion)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 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
DepositionSep 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 6.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3802
Polymers4,2841
Non-polymers961
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.502, 26.209, 31.102
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 6.9 / OcKTx4


Mass: 4284.128 Da / Num. of mol.: 1 / Fragment: residues 24-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opistophthalmus carinatus (scorpion) / Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q6XLL6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM Na Acetate pH 4.5, 200 mM Li2SO4, 50% PEG400

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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: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 2751 / % possible obs: 83.9 % / Redundancy: 1.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.045 / Χ2: 1.981 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.8 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 108 / CC1/2: 0.944 / Rpim(I) all: 0.092 / Χ2: 1.981 / % possible all: 67.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.593 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20506 125 4.5 %RANDOM
Rwork0.13905 ---
obs0.14215 2623 83.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.13 Å2
2---0.34 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms289 0 5 57 351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019299
X-RAY DIFFRACTIONr_bond_other_d0.0040.02275
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.997401
X-RAY DIFFRACTIONr_angle_other_deg0.8113644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.968539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.79223.3339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9791556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.528152
X-RAY DIFFRACTIONr_chiral_restr0.1340.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0254
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_it1.3561.058159
X-RAY DIFFRACTIONr_mcbond_other1.271.049158
X-RAY DIFFRACTIONr_mcangle_it2.0331.752197
X-RAY DIFFRACTIONr_mcangle_other2.031.76198
X-RAY DIFFRACTIONr_scbond_it4.3491.527140
X-RAY DIFFRACTIONr_scbond_other2.1931.458137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4552.218199
X-RAY DIFFRACTIONr_long_range_B_refined8.34612.492340
X-RAY DIFFRACTIONr_long_range_B_other7.52710.665322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 5 -
Rwork0.166 159 -
obs--66.94 %
Refinement TLS params.Method: refined / Origin x: 19.4634 Å / Origin y: 4.3833 Å / Origin z: 4.176 Å
111213212223313233
T0.0022 Å20.0001 Å2-0.0058 Å2-0.0027 Å2-0.0003 Å2--0.0355 Å2
L2.542 °2-0.5288 °2-0.7837 °2-2.1333 °20.044 °2--2.5538 °2
S-0.0281 Å °-0.0187 Å °0.0607 Å °0.0228 Å °0.0121 Å °0.0636 Å °0.0394 Å °0.0031 Å °0.0161 Å °

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