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- PDB-5i9d: Crystal structure of designed pentatricopeptide repeat protein dP... -

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Basic information

Entry
Database: PDB / ID: 5i9d
TitleCrystal structure of designed pentatricopeptide repeat protein dPPR-U8A2 in complex with its target RNA U8A2
Components
  • RNA (5'-R(*GP*GP*GP*G*UP*UP*UP*UP*AP*AP*UP*UP*UP*UP*CP*CP*CP*C)-3')
  • pentatricopeptide repeat protein dPPR-U8A2
KeywordsRNA BINDING PROTEIN/RNA / RNA binding protein / single-stranded RNA / designer pentatricopeptide repeat protein / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsShen, C. / Zhang, D. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.
Authors: Shen, C. / Zhang, D. / Guan, Z. / Liu, Y. / Yang, Z. / Yang, Y. / Wang, X. / Wang, Q. / Zhang, Q. / Fan, S. / Zou, T. / Yin, P.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: pentatricopeptide repeat protein dPPR-U8A2
B: RNA (5'-R(*GP*GP*GP*G*UP*UP*UP*UP*AP*AP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,1272
Polymers57,1272
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-28 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.546, 84.904, 95.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein pentatricopeptide repeat protein dPPR-U8A2


Mass: 51462.609 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)
#2: RNA chain RNA (5'-R(*GP*GP*GP*G*UP*UP*UP*UP*AP*AP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 5664.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.87 Å3/Da / Density % sol: 34.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ethyl Acetate,D-(+)-glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.59→47.7 Å / Num. obs: 13826 / % possible obs: 99.8 % / Redundancy: 8.6 % / Net I/σ(I): 16.7

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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
Starting model: 4PJR

4pjr


Resolution: 2.596→46.082 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 704 5.11 %
Rwork0.2669 --
obs0.2683 13769 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.596→46.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 198 0 41 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153022
X-RAY DIFFRACTIONf_angle_d1.7894098
X-RAY DIFFRACTIONf_dihedral_angle_d19.4421198
X-RAY DIFFRACTIONf_chiral_restr0.104504
X-RAY DIFFRACTIONf_plane_restr0.008474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5956-2.7960.30421280.27942541X-RAY DIFFRACTION99
2.796-3.07730.3071410.2812585X-RAY DIFFRACTION100
3.0773-3.52240.36591280.27422586X-RAY DIFFRACTION100
3.5224-4.43730.23381450.23172620X-RAY DIFFRACTION100
4.4373-46.08910.30091620.28412733X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.6627 Å / Origin y: -1.1204 Å / Origin z: -28.006 Å
111213212223313233
T0.2657 Å2-0.0021 Å2-0.0158 Å2-0.2478 Å20.0048 Å2--0.3099 Å2
L-0.0736 °2-0.1091 °2-0.0772 °2-0.6476 °20.5238 °2--1.7371 °2
S-0.0243 Å °-0.0347 Å °0.0321 Å °0.0199 Å °0.0416 Å °0.0038 Å °0.0814 Å °-0.2067 Å °-0.0095 Å °
Refinement TLS groupSelection details: ALL

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