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

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Basic information

Entry
Database: PDB / ID: 6aty
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsVenom protein 51.1
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homologytoxin activity / extracellular region / Venom protein 51.1
Function and homology information
Biological speciesLychas mucronatus (Chinese swimming scorpion)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
CitationJournal: To Be Published
Title: Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
Authors: Correnti, C. / Gewe, M.M.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Venom protein 51.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2442
Polymers4,1521
Non-polymers921
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Venom protein 51.1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)25,46312
Polymers24,9116
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area7570 Å2
ΔGint-43 kcal/mol
Surface area9230 Å2
MethodPISA
3
A: Venom protein 51.1
hetero molecules

A: Venom protein 51.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4884
Polymers8,3042
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area4530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.775, 39.775, 68.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein/peptide Venom protein 51.1


Mass: 4151.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lychas mucronatus (Chinese swimming scorpion)
Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P0CJ17
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate-citrate pH 4.2, 40% Ethanol, 5% PEG 000

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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: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 10167 / % possible obs: 90 % / Redundancy: 16.9 % / Net I/σ(I): 105.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 11.6 / Num. unique obs: 147 / CC1/2: 0.983 / Rpim(I) all: 0.67 / % possible all: 27.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→34.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.996 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22294 140 4.6 %RANDOM
Rwork0.16614 ---
obs0.16899 2905 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.8→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms280 0 6 38 324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019298
X-RAY DIFFRACTIONr_bond_other_d0.0020.02271
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.978396
X-RAY DIFFRACTIONr_angle_other_deg0.9323633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.734538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.792210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8751551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.469152
X-RAY DIFFRACTIONr_chiral_restr0.1260.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0263
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_it1.6011.001155
X-RAY DIFFRACTIONr_mcbond_other1.5720.993154
X-RAY DIFFRACTIONr_mcangle_it2.5692.207189
X-RAY DIFFRACTIONr_mcangle_other2.5622.226190
X-RAY DIFFRACTIONr_scbond_it2.2441.259143
X-RAY DIFFRACTIONr_scbond_other2.2011.26143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5482.692207
X-RAY DIFFRACTIONr_long_range_B_refined6.09320.106341
X-RAY DIFFRACTIONr_long_range_B_other6.09420.097341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.758 6 -
Rwork0.344 91 -
obs--42.36 %

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