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- PDB-5iwb: Crystal structure of design pentatricopeptide repeat complex with... -

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Basic information

Entry
Database: PDB / ID: 5iwb
TitleCrystal structure of design pentatricopeptide repeat complex with MORF protein
Components
  • Multiple organellar RNA editing factor 9, chloroplastic
  • PLS3-PPR
KeywordsRNA BINDING PROTEIN / pentatricopeptide repeat / complex / MORF
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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å
AuthorsYan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: To be published
Title: Structural basis for designer pentatricopeptide repeat proteins interaction with MORF protein
Authors: Yan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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: PLS3-PPR


Theoretical massNumber of molelcules
Total (without water)30,4342
Polymers30,4342
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-14 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.110, 63.110, 136.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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.: 1 / Fragment: UNP residues 75-196 / Mutation: C12S, C114S
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 PLS3-PPR


Mass: 14980.376 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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Sodium cacodylate trihydrate,Magnesium acetate tetrahydrate,PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→45 Å / Num. obs: 28002 / % possible obs: 99.92 % / Redundancy: 27.6 % / Net I/σ(I): 40.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.764→42.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 1367 4.89 %
Rwork0.179 --
obs0.18 27927 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.764→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 0 288 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061844
X-RAY DIFFRACTIONf_angle_d0.8042495
X-RAY DIFFRACTIONf_dihedral_angle_d15.4631116
X-RAY DIFFRACTIONf_chiral_restr0.05279
X-RAY DIFFRACTIONf_plane_restr0.005317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7643-1.82740.20411180.19752607X-RAY DIFFRACTION100
1.8274-1.90060.22131520.18992591X-RAY DIFFRACTION100
1.9006-1.98710.2321490.18052589X-RAY DIFFRACTION100
1.9871-2.09180.22171250.18032618X-RAY DIFFRACTION100
2.0918-2.22290.21261430.17082614X-RAY DIFFRACTION100
2.2229-2.39450.19141350.17832632X-RAY DIFFRACTION100
2.3945-2.63540.18691220.18572680X-RAY DIFFRACTION100
2.6354-3.01670.18951430.18252659X-RAY DIFFRACTION100
3.0167-3.80030.21091290.17642709X-RAY DIFFRACTION100
3.8003-42.42260.1821510.1742861X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -18.5021 Å / Origin y: 11.7307 Å / Origin z: 5.1512 Å
111213212223313233
T0.1313 Å20.0069 Å20.0106 Å2-0.1188 Å20.006 Å2--0.0725 Å2
L0.9659 °20.3853 °20.5434 °2-0.4259 °20.2882 °2--0.9891 °2
S-0.0216 Å °0.0465 Å °0.0034 Å °-0.0473 Å °0.0335 Å °-0.0329 Å °-0.0502 Å °-0.007 Å °-0.0116 Å °
Refinement TLS groupSelection details: all

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