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- PDB-5i9g: Crystal structure of designed pentatricopeptide repeat protein dP... -

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Basic information

Entry
Database: PDB / ID: 5i9g
TitleCrystal structure of designed pentatricopeptide repeat protein dPPR-U8C2 in complex with its target RNA U8C2
Components
  • RNA (5'-R(*GP*GP*G*GP*UP*UP*UP*UP*CP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')
  • pentatricopeptide repeat protein dPPR-U8C2
KeywordsRNA BINDING PROTEIN/RNA / 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 / Resolution: 2.288 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 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
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
Revision 1.3Mar 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

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Assembly

Deposited unit
C: pentatricopeptide repeat protein dPPR-U8C2
A: RNA (5'-R(*GP*GP*G*GP*UP*UP*UP*UP*CP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,0792
Polymers57,0792
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-40 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.433, 84.782, 94.358
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-U8C2


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*G*GP*UP*UP*UP*UP*CP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 5616.282 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.: 67 / 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: 1.8 Å3/Da / Density % sol: 31.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Bis-Tris propane, Magnesium chloride, Ethyl Acetate, D-(+)-glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9806 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9806 Å / Relative weight: 1
ReflectionResolution: 2.28→40 Å / Num. obs: 18810 / % possible obs: 98.4 % / Redundancy: 6 % / Net I/σ(I): 26.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
HKL-3000data collection
PHASERphasing
RefinementResolution: 2.288→38.668 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.31
RfactorNum. reflection% reflection
Rfree0.2475 909 4.85 %
Rwork0.2251 --
obs0.2261 18753 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.288→38.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 208 0 67 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163119
X-RAY DIFFRACTIONf_angle_d1.8024241
X-RAY DIFFRACTIONf_dihedral_angle_d17.0751229
X-RAY DIFFRACTIONf_chiral_restr0.113521
X-RAY DIFFRACTIONf_plane_restr0.008497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2885-2.43180.29941290.24252572X-RAY DIFFRACTION86
2.4318-2.61950.27641620.23252959X-RAY DIFFRACTION99
2.6195-2.88310.27241600.22553009X-RAY DIFFRACTION100
2.8831-3.30010.21511700.21763006X-RAY DIFFRACTION100
3.3001-4.1570.22851430.20753081X-RAY DIFFRACTION100
4.157-38.67350.25571450.23583217X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.1903 Å / Origin y: 0.4237 Å / Origin z: 18.0266 Å
111213212223313233
T0.3111 Å20.024 Å20.0093 Å2-0.2865 Å2-0.0026 Å2--0.3422 Å2
L0.0653 °2-0.0268 °20.1578 °2-0.482 °2-0.8242 °2--1.8478 °2
S-0.0277 Å °-0.0691 Å °-0.0284 Å °0.0629 Å °-0.0105 Å °-0.0364 Å °-0.071 Å °0.1576 Å °0.0489 Å °
Refinement TLS groupSelection details: ALL

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