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- PDB-5gik: Modulation of the affinity of a HIV-1 capsid-directed ankyrin tow... -

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Basic information

Entry
Database: PDB / ID: 5gik
TitleModulation of the affinity of a HIV-1 capsid-directed ankyrin towards its viral target through critical amino acid editing
ComponentsArtificial ankyrin repeat protein_Ank(GAG)1D4 mutant -S45Y
KeywordsPROTEIN BINDING / DARPins / Designed ankyrin repeat
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. ...Chuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J.
CitationJournal: To Be Published
Title: Modulation of the affinity of a HIV-1 capsid-directed ankyrintowards its viral target through critical amino acid editing
Authors: Chuankhayan, P. / Saoin, S. / Wisitponchai, T. / Intachai, K. / Chupradit, K. / Moonmuang, S. / Kitidee, K. / Nangola, S. / Sanghiran, L.V. / Hong, S.S. / Boulanger, P. / Tayapiwatana, C. / Chen, C.J.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -S45Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9482
Polymers16,8561
Non-polymers921
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-1 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.828, 29.313, 51.291
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -S45Y


Mass: 16855.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#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.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THE STRUCTURE HAS A MUTATION, S45Y.

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 1000, reagent alcohol, sodium-phosphate dibasic/citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.49→53.31 Å / Num. obs: 19525 / % possible obs: 75 % / Redundancy: 3.9 % / Net I/σ(I): 28.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→53.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.524 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20963 1025 5.2 %RANDOM
Rwork0.18667 ---
obs0.18785 18504 74.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.08 Å2
2--0.13 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.49→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 6 128 1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191213
X-RAY DIFFRACTIONr_bond_other_d0.0030.021180
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9631643
X-RAY DIFFRACTIONr_angle_other_deg1.1553.0022700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12824.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.546158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02276
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_it2.3631.962615
X-RAY DIFFRACTIONr_mcbond_other2.3621.957614
X-RAY DIFFRACTIONr_mcangle_it3.3522.928767
X-RAY DIFFRACTIONr_mcangle_other3.352.934768
X-RAY DIFFRACTIONr_scbond_it4.0062.517596
X-RAY DIFFRACTIONr_scbond_other4.0032.518597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0673.578877
X-RAY DIFFRACTIONr_long_range_B_refined7.95317.4161423
X-RAY DIFFRACTIONr_long_range_B_other7.65316.8511380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.494→1.533 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 22 -
Rwork0.188 428 -
obs--23.65 %

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