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- PDB-4n2s: Crystal Structure of THA8 in complex with Zm1a-6 RNA -

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Basic information

Entry
Database: PDB / ID: 4n2s
TitleCrystal Structure of THA8 in complex with Zm1a-6 RNA
Components
  • THA8 RNA binding protein
  • Zm1a-6 RNA
KeywordsSPLICING/RNA / Pentatricopeptide repeat (PPR) protein / small intron RNA binding / Group II intron RNA splicing / 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: 3 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

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Assembly

Deposited unit
A: THA8 RNA binding protein
B: Zm1a-6 RNA


Theoretical massNumber of molelcules
Total (without water)31,5902
Polymers31,5902
Non-polymers00
Water27015
1
A: THA8 RNA binding protein
B: Zm1a-6 RNA

A: THA8 RNA binding protein
B: Zm1a-6 RNA


Theoretical massNumber of molelcules
Total (without water)63,1804
Polymers63,1804
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)88.250, 88.250, 78.927
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 Zm1a-6 RNA


Mass: 3837.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Zm1a-6 RNA sequence is chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG 4000 and 0.1 M MES, pH 6.0, 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: Mar 22, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 6677 / Num. obs: 6677 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 19.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 2.2 / % 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: THA8 Apo structure

Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.639 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23151 315 4.7 %RANDOM
Rwork0.20521 ---
obs0.20651 6334 99.91 %-
all-6340 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.625 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.16 Å20 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 90 0 15 1596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191621
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9172220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5935196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7222.38867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43415240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2431517
X-RAY DIFFRACTIONr_chiral_restr0.0590.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211215
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 24 -
Rwork0.373 390 -
obs--100 %

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