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- PDB-5a0o: adhiron raised against p300 -

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Basic information

Entry
Database: PDB / ID: 5a0o
Titleadhiron raised against p300
ComponentsADHIRON
KeywordsDE NOVO PROTEIN / AFFIMER
Function / homologyNuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsKyle, H.F. / Wickson, K.F. / Stott, J. / Burslem, G.M. / Breeze, A.L. / Tiede, C. / Tomlinson, D.C. / Warriner, S.L. / Nelson, A. / Wilson, A.J. / Edwards, T.A.
CitationJournal: Mol.Biosyst. / Year: 2015
Title: Exploration of the Hif-1Alpha.P300 Interface Using Peptide and Adhiron Phage Display Technologies
Authors: Kyle, H.F. / Wickson, K.F. / Stott, J. / Burslem, G.M. / Breeze, A.L. / Tiede, C. / Tomlinson, D.C. / Warriner, S.L. / Nelson, A. / Wilson, A.J. / Edwards, T.A.
History
DepositionApr 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ADHIRON
S: ADHIRON


Theoretical massNumber of molelcules
Total (without water)24,9302
Polymers24,9302
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9.8 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.290, 72.640, 107.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

21S-2011-

HOH

31S-2012-

HOH

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Components

#1: Protein ADHIRON


Mass: 12465.246 Da / Num. of mol.: 2 / Fragment: ADHIRON
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DESIGNED NON-ANTIBODY BINDING PROTEIN / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 3.67 Å3/Da / Density % sol: 66.5 % / Description: NONE
Crystal growpH: 7 / Details: 0.8 M DI-SODIUM SUCCINATE PH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 2.73→36.73 Å / Num. obs: 7134 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.3
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N6U

4n6u


Resolution: 2.73→36.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.875 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.91 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27811 373 5 %RANDOM
Rwork0.23876 ---
obs0.24058 7134 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.371 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.57 Å2
Refinement stepCycle: LAST / Resolution: 2.73→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 0 48 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191558
X-RAY DIFFRACTIONr_bond_other_d0.0020.021532
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9712095
X-RAY DIFFRACTIONr_angle_other_deg0.85733544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0975184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22125.27872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.09215302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.817154
X-RAY DIFFRACTIONr_chiral_restr0.090.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
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_it1.2987.061742
X-RAY DIFFRACTIONr_mcbond_other1.2997.057741
X-RAY DIFFRACTIONr_mcangle_it2.39910.576924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8637.082813
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 26 -
Rwork0.455 513 -
obs--100 %

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