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- PDB-7dne: DARPin 5m3_D12 in complex with V3-IY (MN) crown mimetic -

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Basic information

Entry
Database: PDB / ID: 7dne
TitleDARPin 5m3_D12 in complex with V3-IY (MN) crown mimetic
Components
  • DARPin 5m3_D12
  • V3-IY (MN) crown mimetic peptide
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / anti-HIV
Biological speciessynthetic construct (others)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, Y. / Plueckthun, A.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_192689 Switzerland
Swiss National Science Foundation310030B_166676 Switzerland
Swiss National Science Foundation31003A_146278 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization.
Authors: Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / ...Authors: Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / Reinberg, T. / Schaefer, J.V. / Karakus, U. / Ursprung, S. / Mann, A. / Rusert, P. / Kouyos, R.D. / Robinson, J.A. / Gunthard, H.F. / Pluckthun, A. / Trkola, A.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DARPin 5m3_D12
B: DARPin 5m3_D12
C: V3-IY (MN) crown mimetic peptide
D: V3-IY (MN) crown mimetic peptide


Theoretical massNumber of molelcules
Total (without water)37,0904
Polymers37,0904
Non-polymers00
Water2,270126
1
A: DARPin 5m3_D12
C: V3-IY (MN) crown mimetic peptide


Theoretical massNumber of molelcules
Total (without water)18,5452
Polymers18,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area8290 Å2
MethodPISA
2
B: DARPin 5m3_D12
D: V3-IY (MN) crown mimetic peptide


Theoretical massNumber of molelcules
Total (without water)18,5452
Polymers18,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-13 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.330, 51.800, 57.210
Angle α, β, γ (deg.)78.970, 80.890, 80.420
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DARPin 5m3_D12


Mass: 16729.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Protein/peptide V3-IY (MN) crown mimetic peptide


Mass: 1815.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30.0% w/v PEG 4000, 0.2M Li2SO4, 0.02M TAPS pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40.951 Å / Num. obs: 21900 / % possible obs: 92.18 % / Redundancy: 3.1 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05681 / Rrim(I) all: 0.06871 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6873 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 2238 / CC1/2: 0.759 / % possible all: 93.07

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 1.9→40.95 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1093 5 %
Rwork0.2324 20766 -
obs0.2342 21859 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.27 Å2 / Biso mean: 47.087 Å2 / Biso min: 18.74 Å2
Refinement stepCycle: final / Resolution: 1.9→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 0 126 2713
Biso mean---40.2 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.37281370.35892633277093
1.99-2.090.41381400.33492646278693
2.09-2.220.34331380.29992617275594
2.22-2.390.34691380.26912622276093
2.39-2.630.26411360.26572599273593
2.63-3.020.29091370.26412597273491
3.02-3.80.2751350.21922552268791
3.8-40.950.18931320.17072500263289

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