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- PDB-5knh: CRYSTAL STRUCTURE OF DARPIN 6G9 IN COMPLEX WITH CYNO IL-13 -

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Basic information

Entry
Database: PDB / ID: 5knh
TitleCRYSTAL STRUCTURE OF DARPIN 6G9 IN COMPLEX WITH CYNO IL-13
Components
  • DARPIN 6G9
  • IL13
KeywordsCYTOKINE/DE NOVO PROTEIN / ALTERNATIVE SCAFFOLD / CYTOKINE-DE NOVO PROTEIN complex
Function / homology
Function and homology information


cytokine receptor binding / cytokine activity / immune response / extracellular space
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Ankyrin repeat-containing domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; ...Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Ankyrin repeat-containing domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Interleukin-13
Similarity search - Component
Biological speciessynthetic construct (others)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTeplyakov, A. / Malia, T. / Obmolova, G. / Gilliland, G.
CitationJournal: Protein Eng. Des. Sel. / Year: 2017
Title: Conformational flexibility of an anti-IL-13 DARPin.
Authors: Teplyakov, A. / Malia, T.J. / Obmolova, G. / Jacobs, S.A. / O'Neil, K.T. / Gilliland, G.L.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DARPIN 6G9
I: IL13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6063
Polymers30,5472
Non-polymers591
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-8 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.410, 78.490, 119.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-1204-

HOH

21D-1214-

HOH

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Components

#1: Protein DARPIN 6G9


Mass: 18244.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein IL13


Mass: 12302.288 Da / Num. of mol.: 1 / Fragment: UNP residues 22-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: IL13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0PW92
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.01 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 11% PEG 3350, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 32998 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.7 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L5X

3l5x


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.299 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.19577 1040 3.2 %RANDOM
Rwork0.16793 ---
obs0.16881 31810 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---1.57 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 4 204 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.972643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40525.9386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57215324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.997157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2315
X-RAY DIFFRACTIONr_gen_planes_refined00.0211457
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.69921263
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.46942012
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it33.14488683
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it31.92188631
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 84 -
Rwork0.206 2300 -
obs--96.4 %

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