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- PDB-4leu: Crystal Structure of THA8-like protein from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4leu
TitleCrystal Structure of THA8-like protein from Arabidopsis thaliana
ComponentsPentatricopeptide repeat-containing protein At3g46870
KeywordsRNA BINDING PROTEIN / Group II intron RNA splicing in chloroplast / RNA-binding protein / Chloroplast / METAL BINDING PROTEIN
Function / homology
Function and homology information


sequence-specific mRNA binding / chloroplast / single-stranded RNA binding / zinc ion binding
Similarity search - Function
Pentatricopeptide repeat-containing protein THA8L-like / PPR repeat family / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Protein THYLAKOID ASSEMBLY 8-like, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKe, J. / Chen, R.Z. / Ban, T. / Brunzelle, J.S. / Gu, X. / Kang, Y. / Melcher, K. / Zhu, J.K. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition.
Authors: Ban, T. / Ke, J. / Chen, R. / Gu, X. / Tan, M.H. / Zhou, X.E. / Kang, Y. / Melcher, K. / Zhu, J.K. / Xu, H.E.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Pentatricopeptide repeat-containing protein At3g46870


Theoretical massNumber of molelcules
Total (without water)30,1841
Polymers30,1841
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.170, 53.302, 42.312
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pentatricopeptide repeat-containing protein At3g46870


Mass: 30183.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g46870, T6H20.100, THA8 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9STF9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12% (w/v) PEG3350, 4% (v/v) Tacsimate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17524 / Num. obs: 17384 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2 / Num. unique all: 2413 / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.79 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.25306 887 5.1 %RANDOM
Rwork0.20406 ---
all0.20659 16642 --
obs0.20659 16394 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-1.37 Å2
2---1.96 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 0 128 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021539
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.0092069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85924.9371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31815312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.083158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211132
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 66 -
Rwork0.283 1080 -
obs--92.42 %

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