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- PDB-5iww: Crystal structure of RNA editing factor of designer PLS-type PPR/... -

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Basic information

Entry
Database: PDB / ID: 5iww
TitleCrystal structure of RNA editing factor of designer PLS-type PPR/9R protein in complex with MORF9/RIP9
Components
  • Multiple organellar RNA editing factor 9, chloroplastic
  • PLS9-PPR
KeywordsRNA BINDING PROTEIN / pentatricopeptide repeat / complex / MORF / PLS-type
Function / homology
Function and homology information


chloroplast RNA modification / cytidine to uridine editing / chloroplast envelope / chloroplast stroma / chloroplast / mRNA processing / protein dimerization activity / mRNA binding / protein homodimerization activity
Similarity search - Function
MORF/ORRM1/DAG-like / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily
Similarity search - Domain/homology
Multiple organellar RNA editing factor 9, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsYan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: Nat Plants / Year: 2017
Title: MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing
Authors: Yan, J. / Zhang, Q. / Guan, Z. / Wang, Q. / Li, L. / Ruan, F. / Lin, R. / Zou, T. / Yin, P.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple organellar RNA editing factor 9, chloroplastic
B: Multiple organellar RNA editing factor 9, chloroplastic
C: Multiple organellar RNA editing factor 9, chloroplastic
D: PLS9-PPR


Theoretical massNumber of molelcules
Total (without water)85,5754
Polymers85,5754
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-41 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.190, 103.190, 149.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Multiple organellar RNA editing factor 9, chloroplastic / RNA editing-interacting protein 9


Mass: 15453.313 Da / Num. of mol.: 3 / Fragment: UNP residues 75-196 / Mutation: C85S, C187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MORF9, RIP9, At1g11430, T23J18.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LPZ1
#2: Protein PLS9-PPR


Mass: 39215.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Magnesium sulfate heptahydrate, 1,3-Bis[tris(hydroxymethyl)methylamino]propane, Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→53 Å / Num. obs: 25740 / % possible obs: 98.5 % / Redundancy: 5.6 % / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data collection
XDSdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→51.595 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2208 1250 4.87 %
Rwork0.1802 --
obs0.1822 25689 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→51.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 0 56 4987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085032
X-RAY DIFFRACTIONf_angle_d0.9426800
X-RAY DIFFRACTIONf_dihedral_angle_d22.5221870
X-RAY DIFFRACTIONf_chiral_restr0.052761
X-RAY DIFFRACTIONf_plane_restr0.005861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.75630.33661400.25972740X-RAY DIFFRACTION100
2.7563-2.88170.26711350.2352762X-RAY DIFFRACTION100
2.8817-3.03360.25511350.2292744X-RAY DIFFRACTION100
3.0336-3.22370.31961460.21742724X-RAY DIFFRACTION99
3.2237-3.47250.28821330.20632733X-RAY DIFFRACTION99
3.4725-3.82190.21861410.18822717X-RAY DIFFRACTION98
3.8219-4.37460.191560.1542663X-RAY DIFFRACTION97
4.3746-5.51060.19971360.14532669X-RAY DIFFRACTION96
5.5106-51.60480.16961280.16222687X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -24.0278 Å / Origin y: 253.1133 Å / Origin z: 6.6838 Å
111213212223313233
T0.513 Å2-0.0247 Å20.0945 Å2-0.4709 Å2-0.0599 Å2--0.4698 Å2
L0.2209 °2-0.2714 °20.1193 °2-0.9222 °2-0.1291 °2--0.039 °2
S0.0361 Å °-0.0351 Å °0.1067 Å °-0.2005 Å °0.0948 Å °-0.2273 Å °0.0146 Å °0.0358 Å °-0.1213 Å °
Refinement TLS groupSelection details: all

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