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- PDB-1n0q: 3ANK: A designed ankyrin repeat protein with three identical cons... -

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Basic information

Entry
Database: PDB / ID: 1n0q
Title3ANK: A designed ankyrin repeat protein with three identical consensus repeats
Components3 ankyrin repeats
KeywordsSTRUCTURAL PROTEIN / ANKYRIN REPEAT / ANK
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / trifluoroacetic acid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMosavi, L.K. / Minor Jr., D.L. / Peng, Z.-Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Consensus-derived structural determinants of the ankyrin repeat motif.
Authors: Mosavi, L.K. / Minor Jr., D.L. / Peng, Z.-Y.
History
DepositionOct 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3 ankyrin repeats
B: 3 ankyrin repeats
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9913
Polymers19,8772
Non-polymers1141
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.636, 43.159, 105.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3 ankyrin repeats / 3ANK


Mass: 9938.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Gene: designed consensus ankyrin repeat / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.0
350 %MPD1reservoir
430 %MPD1drop

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→19.96 Å / Num. all: 43548 / Num. obs: 41302 / % possible obs: 99.52 % / Rsym value: 0.087 / Net I/σ(I): 11.8
Reflection
*PLUS
Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Num. unique obs: 2246 / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ANK

4ank


Resolution: 1.26→19.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18731 2246 5.2 %RANDOM
Rwork0.17136 ---
all0.17136 43548 --
obs0.17218 41302 97.52 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.26→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 6 183 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211411
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9821907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9855182
X-RAY DIFFRACTIONr_chiral_restr0.0810.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021040
X-RAY DIFFRACTIONr_nbd_refined0.2260.2715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.228
X-RAY DIFFRACTIONr_mcbond_it0.7521.5911
X-RAY DIFFRACTIONr_mcangle_it1.41521433
X-RAY DIFFRACTIONr_scbond_it2.7423500
X-RAY DIFFRACTIONr_scangle_it4.3364.5474
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 111
Rwork0.298 1649
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29290.0448-0.04110.8969-0.2132.1069-0.00320.03940.0220.06210.0144-0.024-0.03280.0509-0.01120.02870.0048-0.00690.0033-0.00060.016223.389733.039521.3877
20.9361-0.19310.60091.0746-0.51342.450.03450.049-0.06430.00960.00410.00790.05770.0568-0.03850.0021-0.0012-0.00650.01380.00550.020515.189520.86471.3913
30.26790.02160.31390.21770.21220.8930.00530.0310.01010.05630.01440.0150.00550.0093-0.01970.0347-0.0032-0.00690.02050.00090.044819.156227.404711.6488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 93
2X-RAY DIFFRACTION2B1 - 93
3X-RAY DIFFRACTION3A94 - 189
4X-RAY DIFFRACTION3B3134 - 3220
Refinement
*PLUS
Rfactor Rfree: 0.187 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.41

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