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- PDB-6ay8: Cartilage homing cysteine-dense-peptides -

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Basic information

Entry
Database: PDB / ID: 6ay8
TitleCartilage homing cysteine-dense-peptides
ComponentsPotassium channel toxin alpha-KTx 15.8
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 15.8
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGewe, M.M. / Strong, R.K. / Watson, A.
CitationJournal: To Be Published
Title: Cartilage homing cysteine-dense-peptides
Authors: Gewe, M.M.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 15.8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5274
Polymers4,2391
Non-polymers2883
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)20.240, 34.927, 36.977
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 Potassium channel toxin alpha-KTx 15.8 / BmKKx1 / Neurotoxin Kk4


Mass: 4238.868 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q86BX0
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 33 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium sulfate, 20% PEG 3350

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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 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 2368 / % possible obs: 78.3 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Net I/σ(I): 35.4
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 10 / CC1/2: 0.991 / Rpim(I) all: 0.094 / % possible all: 8.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ATM

6atm


Resolution: 1.78→25.39 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.812 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16451 139 5.9 %RANDOM
Rwork0.10984 ---
obs0.11289 2207 84.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.78→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms290 0 15 33 338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019305
X-RAY DIFFRACTIONr_bond_other_d0.0080.02266
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.972411
X-RAY DIFFRACTIONr_angle_other_deg1.083609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.968539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.84820.71414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5721549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.703156
X-RAY DIFFRACTIONr_chiral_restr0.110.245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02343
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0267
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_it0.6730.909159
X-RAY DIFFRACTIONr_mcbond_other0.6670.906158
X-RAY DIFFRACTIONr_mcangle_it0.9311.354197
X-RAY DIFFRACTIONr_mcangle_other0.9321.357198
X-RAY DIFFRACTIONr_scbond_it1.5981.246146
X-RAY DIFFRACTIONr_scbond_other1.121.079131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6661.56195
X-RAY DIFFRACTIONr_long_range_B_refined3.58511.643329
X-RAY DIFFRACTIONr_long_range_B_other3.58911.312321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.778→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 5 -
Rwork0.137 42 -
obs--22.71 %

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