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- PDB-3odv: X-ray structure of kaliotoxin by racemic protein crystallography -

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Basic information

Entry
Database: PDB / ID: 3odv
TitleX-ray structure of kaliotoxin by racemic protein crystallography
ComponentsPotassium channel toxin alpha-KTx 3.1
KeywordsTOXIN / Racemic protein / Direct methods / chemical synthesis
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
CITRIC ACID / trifluoroacetic acid / Potassium channel toxin alpha-KTx 3.1
Similarity search - Component
Biological speciesAndroctonus mauretanicus mauretanicus (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å
AuthorsPentelute, B.L. / Mandal, K. / Gates, Z.P. / Sawaya, M.R. / Yeates, T.O. / Kent, S.B.H.
CitationJournal: Chem.Commun.(Camb.) / Year: 2010
Title: Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography.
Authors: Pentelute, B.L. / Mandal, K. / Gates, Z.P. / Sawaya, M.R. / Yeates, T.O. / Kent, S.B.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 3.1
B: Potassium channel toxin alpha-KTx 3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9426
Polymers8,3302
Non-polymers6124
Water1,62190
1
A: Potassium channel toxin alpha-KTx 3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2792
Polymers4,1651
Non-polymers1141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Potassium channel toxin alpha-KTx 3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6634
Polymers4,1651
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.150, 30.511, 41.097
Angle α, β, γ (deg.)109.39, 97.39, 97.09
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 3.1 / Kaliotoxin-1 / KTX-1


Mass: 4165.052 Da / Num. of mol.: 2 / Fragment: L-Kaliotoxin / Source method: obtained synthetically / Details: Chemical Synthesis
Source: (synth.) Androctonus mauretanicus mauretanicus (scorpion)
References: UniProt: P24662
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.74 Å3/Da / Density % sol: 29.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. all: 62285 / Num. obs: 62285 / % possible obs: 88.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.9
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3600 / % possible all: 50.9

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.95→38.13 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.469 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20326 3130 5 %RANDOM
Rwork0.188 ---
obs0.18878 59134 87.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.12 Å2-0.21 Å2
2---0.53 Å20.1 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 0.95→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 40 90 696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022840
X-RAY DIFFRACTIONr_bond_other_d0.0010.02674
X-RAY DIFFRACTIONr_angle_refined_deg1.6462.0581142
X-RAY DIFFRACTIONr_angle_other_deg0.87231666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4465118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98821.48127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91915194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.498159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_mcbond_it1.6321.5496
X-RAY DIFFRACTIONr_mcbond_other0.4491.5193
X-RAY DIFFRACTIONr_mcangle_it2.5612821
X-RAY DIFFRACTIONr_scbond_it3.4833344
X-RAY DIFFRACTIONr_scangle_it5.1614.5306
X-RAY DIFFRACTIONr_rigid_bond_restr1.23231514
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.553 111 -
Rwork0.494 2262 -
obs--45.08 %

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