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- PDB-6av8: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 6av8
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsU5-theraphotoxin-Hs1b 1
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / carbohydrate binding / extracellular region / U5-theraphotoxin-Hs1b 1
Function and homology information
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 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 / 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 1.3Oct 16, 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: U5-theraphotoxin-Hs1b 1


Theoretical massNumber of molelcules
Total (without water)3,8771
Polymers3,8771
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.639, 50.639, 20.104
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein/peptide U5-theraphotoxin-Hs1b 1 / U5-TRTX-Hs1b / Lectin SHL-Ib1


Mass: 3877.481 Da / Num. of mol.: 1 / Fragment: residues 50-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma schmidti (Chinese earth tiger)
Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: B3FIS6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 citrate pH = 5, 20% w/w PEG 6000

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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: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 2417 / % possible obs: 97.5 % / Redundancy: 25.9 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.059 / Net I/σ(I): 58.11
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.286 / Num. unique obs: 94 / CC1/2: 0.941 / Rpim(I) all: 0.118 / % possible all: 80.3

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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: 1QK7

1qk7


Resolution: 1.89→43.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.327 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26723 107 4.6 %RANDOM
Rwork0.21572 ---
obs0.21801 2207 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.265 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.43 Å20 Å2
2---0.87 Å20 Å2
3---2.81 Å2
Refinement stepCycle: 1 / Resolution: 1.89→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms228 0 0 18 246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02241
X-RAY DIFFRACTIONr_bond_other_d0.0040.02191
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.911329
X-RAY DIFFRACTIONr_angle_other_deg0.9253444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.748528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.02209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4761530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.086151
X-RAY DIFFRACTIONr_chiral_restr0.1130.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0263
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_it2.4312.587115
X-RAY DIFFRACTIONr_mcbond_other2.3882.573114
X-RAY DIFFRACTIONr_mcangle_it3.5314.346142
X-RAY DIFFRACTIONr_mcangle_other3.5244.358143
X-RAY DIFFRACTIONr_scbond_it2.9312.654126
X-RAY DIFFRACTIONr_scbond_other2.9192.659127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3024.363188
X-RAY DIFFRACTIONr_long_range_B_refined5.31721.211289
X-RAY DIFFRACTIONr_long_range_B_other5.31821.213289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 8 -
Rwork0.492 138 -
obs--76.44 %
Refinement TLS params.Method: refined / Origin x: -18.4892 Å / Origin y: 2.8446 Å / Origin z: 1.8036 Å
111213212223313233
T0.051 Å20.0257 Å2-0.0098 Å2-0.0334 Å20.0144 Å2--0.0253 Å2
L9.697 °21.0038 °2-0.4685 °2-2.8416 °20.5123 °2--3.5364 °2
S0.1704 Å °0.1823 Å °0.262 Å °-0.1713 Å °-0.2442 Å °-0.0749 Å °-0.1159 Å °0.045 Å °0.0738 Å °

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