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- PDB-5gi0: Crystal structure of RNA editing factor MORF9/RIP9 -

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Basic information

Entry
Database: PDB / ID: 5gi0
TitleCrystal structure of RNA editing factor MORF9/RIP9
ComponentsMultiple organellar RNA editing factor 9, chloroplastic
KeywordsRNA BINDING PROTEIN / RNA editing factor / MORF9 / RIP9
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 / : / Multiple organellar RNA editing factor 1, MORF domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.044 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
DepositionJun 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple organellar RNA editing factor 9, chloroplastic


Theoretical massNumber of molelcules
Total (without water)15,7351
Polymers15,7351
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.812, 50.690, 38.318
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15734.685 Da / Num. of mol.: 1 / Mutation: C13S, C115S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: sodium bromide,sodium thiocyanate, PEG 3350, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979305 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979305 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 9121 / % possible obs: 99.47 % / Redundancy: 8.9 % / Net I/σ(I): 32.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.044→29.87 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2352 450 4.94 %
Rwork0.2018 --
obs0.2035 9116 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.044→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 0 53 1027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071003
X-RAY DIFFRACTIONf_angle_d0.941365
X-RAY DIFFRACTIONf_dihedral_angle_d13.71594
X-RAY DIFFRACTIONf_chiral_restr0.054145
X-RAY DIFFRACTIONf_plane_restr0.006175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0444-2.34010.28671490.2092859X-RAY DIFFRACTION100
2.3401-2.94790.26941530.22722901X-RAY DIFFRACTION100
2.9479-29.8730.21011480.19052906X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.8742 Å / Origin y: 35.2392 Å / Origin z: 12.4412 Å
111213212223313233
T0.2217 Å20.0145 Å20.0235 Å2-0.2173 Å20.0265 Å2--0.2366 Å2
L0.2657 °2-0.2868 °20.2315 °2-0.4238 °2-0.0862 °2--0.4681 °2
S0.025 Å °0.0866 Å °0.0679 Å °-0.0479 Å °-0.1324 Å °-0.0349 Å °-0.0085 Å °0.0372 Å °-0 Å °
Refinement TLS groupSelection details: all

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