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- PDB-9kbu: Crystal structure of an ankyrin protein -

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Basic information

Entry
Database: PDB / ID: 9kbu
TitleCrystal structure of an ankyrin protein
ComponentsAnkyrin
KeywordsDNA BINDING PROTEIN / DARPins / ankyrin / G-quadruplex / DNA-binding protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNgo, K.H. / Heddi, B. / Winnerdy, F.R. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (MoE, Singapore)MOE2018-T2-2-029 Singapore
Citation
Journal: To Be Published
Title: X-ray structure of a G-quadruplex-ankyrin complex
Authors: Ngo, K.H. / Heddi, B. / Winnerdy, F.R. / Phan, A.T.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin
B: Ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,46814
Polymers36,3852
Non-polymers1,08412
Water5,008278
1
A: Ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5786
Polymers18,1921
Non-polymers3855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8918
Polymers18,1921
Non-polymers6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.545, 119.545, 59.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 13 through 19 or resid 21...
d_2ens_1(chain "B" and (resid 13 through 19 or resid 21...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPLEULEUAA13 - 1913 - 19
d_12ALAALALEULEUAA21 - 3321 - 33
d_13ALAALAALAALAAA35 - 4235 - 42
d_14ASPASPGLUGLUAA44 - 9744 - 97
d_15LEULEUALAALAAA99 - 10499 - 104
d_16VALVALALAALAAA106 - 108106 - 108
d_17ASPASPLEULEUAA110 - 117110 - 117
d_18LEULEUHISHISAA119 - 125119 - 125
d_19GLUGLUGLUGLUAA127 - 130127 - 130
d_110LEULEULYSLYSAA132 - 147132 - 147
d_111ALAALAILEILEAA149 - 152149 - 152
d_112ILEILEGLUGLUAA154 - 159154 - 159
d_113LEULEULEULEUAA161 - 165161 - 165
d_114LYSLYSASNASNAA167 - 169167 - 169
d_21ASPASPLEULEUBB13 - 1913 - 19
d_22ALAALALEULEUBB21 - 3321 - 33
d_23ALAALAALAALABB35 - 4235 - 42
d_24ASPASPGLUGLUBB44 - 9744 - 97
d_25LEULEUALAALABB99 - 10499 - 104
d_26VALVALALAALABB106 - 108106 - 108
d_27ASPASPLEULEUBB110 - 117110 - 117
d_28LEULEUHISHISBB119 - 125119 - 125
d_29GLUGLUGLUGLUBB127 - 130127 - 130
d_210LEULEULYSLYSBB132 - 147132 - 147
d_211ALAALAILEILEBB149 - 152149 - 152
d_212ILEILEGLUGLUBB154 - 159154 - 159
d_213LEULEULEULEUBB161 - 165161 - 165
d_214LYSLYSASNASNBB167 - 169167 - 169

NCS oper: (Code: givenMatrix: (-0.904028701403, -0.22170199056, 0.365486435346), (-0.259255136533, -0.395445446133, -0.881141119977), (0.339880686744, -0.891331098142, 0.300016653311)Vector: -94. ...NCS oper: (Code: given
Matrix: (-0.904028701403, -0.22170199056, 0.365486435346), (-0.259255136533, -0.395445446133, -0.881141119977), (0.339880686744, -0.891331098142, 0.300016653311)
Vector: -94.5244465528, 2.30557459668, 27.8532215625)

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Components

#1: Protein Ankyrin


Mass: 18192.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl pH 8.5, 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.798→59.773 Å / Num. obs: 45789 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 32.14 Å2 / CC1/2: 1 / Net I/σ(I): 22.6
Reflection shellResolution: 1.798→1.829 Å / Num. unique obs: 4525 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJ0

1mj0


Resolution: 1.8→39.13 Å / SU ML: 0.2011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 2310 5.05 %
Rwork0.1758 43473 -
obs0.1768 45783 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 58 278 2724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022540
X-RAY DIFFRACTIONf_angle_d1.12313470
X-RAY DIFFRACTIONf_chiral_restr0.0677401
X-RAY DIFFRACTIONf_plane_restr0.0088452
X-RAY DIFFRACTIONf_dihedral_angle_d16.0077924
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.25114792062 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.29591410.28562681X-RAY DIFFRACTION100
1.84-1.880.3251410.26442703X-RAY DIFFRACTION100
1.88-1.930.25981360.25192698X-RAY DIFFRACTION99.96
1.93-1.980.22891470.22592670X-RAY DIFFRACTION100
1.98-2.040.25651370.2152701X-RAY DIFFRACTION99.89
2.04-2.10.26931680.22482669X-RAY DIFFRACTION100
2.1-2.180.28831450.21792699X-RAY DIFFRACTION100
2.18-2.260.25451650.20422688X-RAY DIFFRACTION100
2.26-2.370.24161590.20512683X-RAY DIFFRACTION100
2.37-2.490.22021490.20252721X-RAY DIFFRACTION100
2.49-2.650.19271460.18862695X-RAY DIFFRACTION100
2.65-2.850.18861220.19022749X-RAY DIFFRACTION100
2.85-3.140.21351300.18272745X-RAY DIFFRACTION100
3.14-3.590.18721560.15752740X-RAY DIFFRACTION100
3.6-4.530.13991370.13492758X-RAY DIFFRACTION100
4.53-39.130.15621310.14952873X-RAY DIFFRACTION99.93

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