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- PDB-6ay7: Cartilage homing cysteine-dense-peptides -

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Basic information

Entry
Database: PDB / ID: 6ay7
TitleCartilage homing cysteine-dense-peptides
ComponentsPotassium channel toxin alpha-KTx 3.5
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 superfamily
Similarity search - Domain/homology
trifluoroacetic acid / Potassium channel toxin alpha-KTx 3.5
Similarity search - Component
Biological speciesAndroctonus australis (Sahara scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsGewe, M.M. / Strong, R.K.
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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 3.5
B: Potassium channel toxin alpha-KTx 3.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2859
Polymers8,6982
Non-polymers5877
Water1,58588
1
A: Potassium channel toxin alpha-KTx 3.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6915
Polymers4,3491
Non-polymers3424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Potassium channel toxin alpha-KTx 3.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5954
Polymers4,3491
Non-polymers2463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.838, 47.125, 48.538
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 3.5 / Kaliotoxin-2 / KTX-2


Mass: 4349.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Androctonus australis (Sahara scorpion)
Gene: KTX2 / Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P45696
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.83 Å3/Da / Density % sol: 32.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Na chloride, 0.1M Phosphate-citrate pH 4.2, 20% PEG 8000

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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 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 5643 / % possible obs: 80.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Net I/σ(I): 32.4
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 34 / CC1/2: 0.995 / Rpim(I) all: 0.106 / % possible all: 9.9

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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: 1.77→33.81 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.281 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19262 304 5.4 %RANDOM
Rwork0.13969 ---
obs0.14268 5310 85.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.77→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms592 0 31 88 711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019629
X-RAY DIFFRACTIONr_bond_other_d0.0010.02560
X-RAY DIFFRACTIONr_angle_refined_deg1.5282.014843
X-RAY DIFFRACTIONr_angle_other_deg0.87131285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.124575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.66117.14328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59715106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8481516
X-RAY DIFFRACTIONr_chiral_restr0.4070.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021685
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02147
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_it1.9611.558309
X-RAY DIFFRACTIONr_mcbond_other1.941.55308
X-RAY DIFFRACTIONr_mcangle_it2.8782.586381
X-RAY DIFFRACTIONr_mcangle_other2.8822.594382
X-RAY DIFFRACTIONr_scbond_it4.8312.465320
X-RAY DIFFRACTIONr_scbond_other4.6192.412296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1293.68426
X-RAY DIFFRACTIONr_long_range_B_refined9.61616.309648
X-RAY DIFFRACTIONr_long_range_B_other9.64215.432622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.775→1.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 5 -
Rwork0.182 67 -
obs--14.97 %

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