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- PDB-5eid: AKR2A ankyrin repeat domain -

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Basic information

Entry
Database: PDB / ID: 5eid
TitleAKR2A ankyrin repeat domain
ComponentsAnkyrin repeat domain-containing protein 2
KeywordsPROTEIN TRANSPORT / AKR2A / ankyrin repeat domain / cytosolic targeting factor
Function / homology
Function and homology information


chloroplast targeting sequence binding / protein targeting to chloroplast / chloroplast outer membrane / glycolipid binding / nucleus / cytoplasm
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...STI1/HOP, DP domain / STI1/HOP, DP domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat domain-containing protein 2A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPu, H. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation31300634 China
CitationJournal: To Be Published
Title: structure of AKR2A ankyrin repeat domain at 2.0 angstroms resolution
Authors: Pu, H. / Li, H.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)17,8151
Polymers17,8151
Non-polymers00
Water61334
1
A: Ankyrin repeat domain-containing protein 2

A: Ankyrin repeat domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)35,6302
Polymers35,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Unit cell
Length a, b, c (Å)124.141, 39.193, 28.499
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ankyrin repeat domain-containing protein 2 / AtAKR2


Mass: 17814.779 Da / Num. of mol.: 1 / Fragment: UNP residues 211-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKR2, AFT, At4g35450, F15J1.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SAR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.06 M Ammonium sulfate, 0.05 M Sodium acetate trihydrate, 33% Polyethylene glycol 4000, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9423 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.514 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQD
Resolution: 2→37.354 Å / FOM work R set: 0.7972 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 430 4.73 %
Rwork0.1872 8664 -
obs0.1895 9094 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.06 Å2 / Biso mean: 30.91 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2→37.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 34 923
Biso mean---35.53 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007904
X-RAY DIFFRACTIONf_angle_d1.0631226
X-RAY DIFFRACTIONf_chiral_restr0.065147
X-RAY DIFFRACTIONf_plane_restr0.006162
X-RAY DIFFRACTIONf_dihedral_angle_d13.736322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28940.27311520.21272882X-RAY DIFFRACTION98
2.2894-2.88430.26711410.20672899X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 20.4142 Å / Origin y: -11.3217 Å / Origin z: 3.919 Å
111213212223313233
T0.2994 Å2-0.0125 Å20.0122 Å2-0.1245 Å20.0054 Å2--0.1466 Å2
L1.4565 °2-0.0565 °20.0669 °2-0.5988 °20.332 °2--0.8239 °2
S0.037 Å °-0.083 Å °0.063 Å °0.0056 Å °-0.0145 Å °0.0498 Å °0.0111 Å °-0.0932 Å °-0.0243 Å °
Refinement TLS groupSelection details: all

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