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- PDB-5i9f: Crystal structure of designed pentatricopeptide repeat protein dP... -

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Basic information

Entry
Database: PDB / ID: 5i9f
TitleCrystal structure of designed pentatricopeptide repeat protein dPPR-U10 in complex with its target RNA U10
Components
  • RNA (5'-R(*GP*GP*GP*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')
  • pentatricopeptide repeat protein dPPR-U10
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 / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsShen, C. / Zhang, D. / Guan, Z. / Zou, T. / Yin, Y.
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-U10
F: RNA (5'-R(*GP*GP*GP*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,1372
Polymers57,1372
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-37 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.732, 85.266, 95.104
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-U10


Mass: 51518.629 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*GP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 5618.250 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.: 76 / 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: 34.26 %
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: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection% possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 21.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PJR

4pjr


Resolution: 2.194→38.903 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.36
RfactorNum. reflection% reflection
Rfree0.2994 1088 4.89 %
Rwork0.2503 --
obs0.2527 22260 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.194→38.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 204 0 76 3270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013248
X-RAY DIFFRACTIONf_angle_d1.2414414
X-RAY DIFFRACTIONf_dihedral_angle_d17.3611279
X-RAY DIFFRACTIONf_chiral_restr0.058536
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29410.33331130.29632536X-RAY DIFFRACTION96
2.2941-2.4150.34191140.2882663X-RAY DIFFRACTION100
2.415-2.56630.34711570.29762616X-RAY DIFFRACTION100
2.5663-2.76440.37931400.28632639X-RAY DIFFRACTION100
2.7644-3.04250.31191240.26292655X-RAY DIFFRACTION100
3.0425-3.48250.31061470.25642676X-RAY DIFFRACTION100
3.4825-4.38670.28271550.2082667X-RAY DIFFRACTION99
4.3867-38.90910.26771380.24922720X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -10.1919 Å / Origin y: -1.2612 Å / Origin z: 27.6809 Å
111213212223313233
T0.3078 Å20.017 Å2-0.0284 Å2-0.3427 Å2-0.0014 Å2--0.3875 Å2
L0.0425 °20.4113 °2-0.1953 °2-0.84 °2-0.4723 °2--2.4826 °2
S-0.0638 Å °0.027 Å °0.0064 Å °-0.0608 Å °0.0381 Å °-0.0766 Å °0.1633 Å °0.2354 Å °0.0218 Å °
Refinement TLS groupSelection details: ALL

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