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- PDB-6au7: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 6au7
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin gamma-KTx 2.2
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyScorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin gamma-KTx 2.2
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 30, 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 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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 gamma-KTx 2.2
B: Potassium channel toxin gamma-KTx 2.2
C: Potassium channel toxin gamma-KTx 2.2
D: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,19210
Polymers16,6234
Non-polymers5686
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-61 kcal/mol
Surface area7530 Å2
MethodPISA
2
A: Potassium channel toxin gamma-KTx 2.2
B: Potassium channel toxin gamma-KTx 2.2
C: Potassium channel toxin gamma-KTx 2.2
D: Potassium channel toxin gamma-KTx 2.2
hetero molecules

A: Potassium channel toxin gamma-KTx 2.2
B: Potassium channel toxin gamma-KTx 2.2
C: Potassium channel toxin gamma-KTx 2.2
D: Potassium channel toxin gamma-KTx 2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,38320
Polymers33,2468
Non-polymers1,13712
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10320 Å2
ΔGint-169 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.173, 48.146, 50.271
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: -1 - 36 / Label seq-ID: 1 - 38

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein/peptide
Potassium channel toxin gamma-KTx 2.2 / BmKK7 / BmKKx2


Mass: 4155.808 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Production host: Homo sapiens (human) / References: UniProt: P59938
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.75 Å3/Da / Density % sol: 29.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.17M AmSO4, 25.5% PEG 4000

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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: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 7571 / % possible obs: 83.1 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 195 / % possible all: 11.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J5J

1j5j


Resolution: 1.9→48.07 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.303 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21869 415 5.5 %RANDOM
Rwork0.20219 ---
obs0.2031 7156 83.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.02 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 32 43 1219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191206
X-RAY DIFFRACTIONr_bond_other_d0.0010.021079
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9821621
X-RAY DIFFRACTIONr_angle_other_deg0.85332501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.69521.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17715197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3481512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211347
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
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_it1.4341.386605
X-RAY DIFFRACTIONr_mcbond_other1.4321.385604
X-RAY DIFFRACTIONr_mcangle_it2.2723.099751
X-RAY DIFFRACTIONr_mcangle_other2.2713.101752
X-RAY DIFFRACTIONr_scbond_it2.1021.66600
X-RAY DIFFRACTIONr_scbond_other2.1011.66600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4523.593870
X-RAY DIFFRACTIONr_long_range_B_refined5.19725.4141259
X-RAY DIFFRACTIONr_long_range_B_other5.19725.4091259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A21540.11
12B21540.11
21A21000.13
22C21000.13
31A21540.09
32D21540.09
41B21700.11
42C21700.11
51B21880.09
52D21880.09
61C21360.11
62D21360.11
LS refinement shellResolution: 1.904→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 6 -
Rwork0.235 121 -
obs--18.54 %

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