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- PDB-4n2q: Crystal structure of THA8 in complex with Zm4 RNA -

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Basic information

Entry
Database: PDB / ID: 4n2q
TitleCrystal structure of THA8 in complex with Zm4 RNA
Components
  • RNA (5'-R(*AP*AP*GP*AP*AP*GP*AP*AP*AP*UP*UP*GP*G)-3')
  • THA8 RNA binding protein
KeywordsSPLICING/RNA / Pentatricopeptide repeat (PPR) protein / Group II intron RNA splicing / small intron RNA / chloroplast / SPLICING-RNA complex
Function / homology
Function and homology information


Group II intron splicing / chloroplast organization / RNA binding / identical protein binding
Similarity search - Function
Protein THYLAKOID ASSEMBLY 8-like / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Pentacotripeptide-repeat region of PRORP domain-containing protein
Similarity search - Component
Biological speciesBrachypodium distachyon (stiff brome)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKe, J. / Chen, R.Z. / Ban, T. / Zhou, X.E. / Gu, X. / Brunzelle, J.S. / Zhu, J.K. / Melcher, K. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for RNA recognition by a dimeric PPR-protein complex.
Authors: Ke, J. / Chen, R.Z. / Ban, T. / Zhou, X.E. / Gu, X. / Tan, M.H. / Chen, C. / Kang, Y. / Brunzelle, J.S. / Zhu, J.K. / Melcher, K. / Xu, H.E.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THA8 RNA binding protein
B: RNA (5'-R(*AP*AP*GP*AP*AP*GP*AP*AP*AP*UP*UP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)32,0052
Polymers32,0052
Non-polymers00
Water25214
1
A: THA8 RNA binding protein
B: RNA (5'-R(*AP*AP*GP*AP*AP*GP*AP*AP*AP*UP*UP*GP*G)-3')

A: THA8 RNA binding protein
B: RNA (5'-R(*AP*AP*GP*AP*AP*GP*AP*AP*AP*UP*UP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)64,0114
Polymers64,0114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
Unit cell
Length a, b, c (Å)90.341, 90.341, 81.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThis is a heterotetramer composed of two protein chains and two RNA chains.

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Components

#1: Protein THA8 RNA binding protein


Mass: 27752.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachypodium distachyon (stiff brome) / Gene: BRADI2G00245, BRADI2G00270 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: I1HB13
#2: RNA chain RNA (5'-R(*AP*AP*GP*AP*AP*GP*AP*AP*AP*UP*UP*GP*G)-3')


Mass: 4252.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The RNA sequence is chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG 4000 and 0.1 M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 8811 / Num. obs: 8811 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo THA8 structure

Resolution: 2.8→45.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.079 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 415 4.7 %RANDOM
Rwork0.205 ---
obs0.207 8359 99.9 %-
all-8365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0 Å2-0 Å2
2---1.82 Å2-0 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 91 0 14 1605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191630
X-RAY DIFFRACTIONr_bond_other_d0.0010.021506
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9182231
X-RAY DIFFRACTIONr_angle_other_deg0.78133454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1255197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60922.568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7921517
X-RAY DIFFRACTIONr_chiral_restr0.0530.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9638.879791
X-RAY DIFFRACTIONr_mcbond_other5.9568.873790
X-RAY DIFFRACTIONr_mcangle_it8.65913.311987
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.1539.947839
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 26 -
Rwork0.309 594 -
obs--100 %

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