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

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Basic information

Entry
Database: PDB / ID: 6ava
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsInsectotoxin-I1
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyScorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily profile. / Knottin, scorpion toxin-like superfamily / : / toxin activity / extracellular region / Insectotoxin-I1
Function and homology information
Biological speciesMesobuthus eupeus (lesser Asian scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insectotoxin-I1
B: Insectotoxin-I1


Theoretical massNumber of molelcules
Total (without water)8,3202
Polymers8,3202
Non-polymers00
Water1,38777
1
A: Insectotoxin-I1


Theoretical massNumber of molelcules
Total (without water)4,1601
Polymers4,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Insectotoxin-I1


Theoretical massNumber of molelcules
Total (without water)4,1601
Polymers4,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.437, 41.437, 88.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-133-

HOH

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Components

#1: Protein/peptide Insectotoxin-I1


Mass: 4159.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus eupeus (lesser Asian scorpion)
Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P15220
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 100 mM Na Acetate pH 4.5, 600 mM AmPO4

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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: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 4317 / % possible obs: 100 % / Redundancy: 58.4 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.021 / Net I/σ(I): 44.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 59.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 26.7 / Num. unique obs: 409 / CC1/2: 0.993 / Rpim(I) all: 0.049 / Χ2: 2.488 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SIS

1sis


Resolution: 2.2→37.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.766 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23558 231 5.4 %RANDOM
Rwork0.17217 ---
obs0.17545 4048 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 0 77 633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019574
X-RAY DIFFRACTIONr_bond_other_d0.0020.02511
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.985769
X-RAY DIFFRACTIONr_angle_other_deg0.92231191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.387573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.98921.81822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6815100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.111156
X-RAY DIFFRACTIONr_chiral_restr0.0710.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02131
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_it0.4540.889298
X-RAY DIFFRACTIONr_mcbond_other0.4530.888297
X-RAY DIFFRACTIONr_mcangle_it0.8611.324369
X-RAY DIFFRACTIONr_mcangle_other0.8611.325370
X-RAY DIFFRACTIONr_scbond_it0.1830.886276
X-RAY DIFFRACTIONr_scbond_other0.1840.881273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3861.321399
X-RAY DIFFRACTIONr_long_range_B_refined4.6287.882660
X-RAY DIFFRACTIONr_long_range_B_other4.1347.169627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 17 -
Rwork0.102 293 -
obs--99.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23081.4163-1.12771.7571-1.29013.6562-0.08-0.0672-0.1721-0.0589-0.0126-0.07590.15990.09430.09260.02630.01210.00680.0139-0.00490.0238-15.1798-4.1315-10.6716
23.5233-0.35980.63473.109-0.94255.6810.0619-0.18130.14230.1341-0.1289-0.0373-0.3827-0.01630.0670.0546-0.00170.01120.0196-0.00750.0283-19.80326.35020.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 38
2X-RAY DIFFRACTION2B2 - 38

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