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- PDB-4qfv: Crystal structure of a unique ankyrin -

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Basic information

Entry
Database: PDB / ID: 4qfv
TitleCrystal structure of a unique ankyrin
ComponentsANK-N5C-281
KeywordsDE NOVO PROTEIN / DESIGNED ANKYRIN REPEATS / DOMAIN SWAP
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsEthayathulla, A.S. / Tikhonova, E.B. / Guan, L.
CitationJournal: Sci Rep / Year: 2015
Title: A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen.
Authors: Tikhonova, E.B. / Ethayathulla, A.S. / Su, Y. / Hariharan, P. / Xie, S. / Guan, L.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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: ANK-N5C-281
B: ANK-N5C-281
C: ANK-N5C-281
D: ANK-N5C-281
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6237
Polymers100,4464
Non-polymers1773
Water10,305572
1
A: ANK-N5C-281
B: ANK-N5C-281
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3414
Polymers50,2232
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-24 kcal/mol
Surface area20990 Å2
MethodPISA
2
C: ANK-N5C-281
D: ANK-N5C-281
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2823
Polymers50,2232
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-22 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.669, 92.748, 69.636
Angle α, β, γ (deg.)90.00, 91.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ANK-N5C-281


Mass: 25111.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 MM SODIUM ACETATE TRIHYDRATE (PH 4.5), 200 MM (NH4)2SO4, 16-18% PEG 3350, AND 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014 / Details: Mirrors
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 56819 / Num. obs: 56375 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 2735 / Rsym value: 0.5 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O60

4o60


Resolution: 1.999→48.735 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.07 / Stereochemistry target values: ML / Details: TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1943 3.54 %RANDOM
Rwork0.1788 ---
all0.181 56819 --
obs0.1804 54876 95.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→48.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 12 572 7390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076973
X-RAY DIFFRACTIONf_angle_d1.0459425
X-RAY DIFFRACTIONf_dihedral_angle_d13.2362575
X-RAY DIFFRACTIONf_chiral_restr0.0481098
X-RAY DIFFRACTIONf_plane_restr0.0061252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.04910.28091080.21753123X-RAY DIFFRACTION79
2.0491-2.10460.3031130.21093432X-RAY DIFFRACTION86
2.1046-2.16650.26181290.20713547X-RAY DIFFRACTION90
2.1665-2.23640.26151320.20623707X-RAY DIFFRACTION94
2.2364-2.31630.23021470.19133804X-RAY DIFFRACTION97
2.3163-2.40910.25921380.19333835X-RAY DIFFRACTION98
2.4091-2.51870.2541470.1943887X-RAY DIFFRACTION99
2.5187-2.65150.21951480.18823907X-RAY DIFFRACTION99
2.6515-2.81760.27021350.19833902X-RAY DIFFRACTION99
2.8176-3.03510.27951580.19773942X-RAY DIFFRACTION99
3.0351-3.34050.23041450.18593921X-RAY DIFFRACTION100
3.3405-3.82370.17071520.15653926X-RAY DIFFRACTION100
3.8237-4.81680.19211420.14943974X-RAY DIFFRACTION100
4.8168-48.74970.17371490.16054026X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.2352 Å / Origin y: 7.0529 Å / Origin z: 102.4424 Å
111213212223313233
T0.1262 Å2-0.0031 Å20.0025 Å2-0.1908 Å2-0.0049 Å2--0.1249 Å2
L0.7614 °2-0.0011 °20.1017 °2-0.1843 °2-0.0072 °2--0.2179 °2
S0.0002 Å °-0.0143 Å °0.0073 Å °0.0144 Å °0.004 Å °0.0066 Å °-0.015 Å °-0.028 Å °-0.0062 Å °
Refinement TLS groupSelection details: all

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