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- PDB-4wn4: Crystal structure of designed cPPR-polyA protein -

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Basic information

Entry
Database: PDB / ID: 4wn4
TitleCrystal structure of designed cPPR-polyA protein
ComponentsPentatricopeptide repeat protein
KeywordsDE NOVO PROTEIN / designer RNA-binding proteins / pentatricopeptide repeat / synthetic biology / RNA-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsCoquille, S.C. / Filipovska, A. / Chia, T.S. / Rajappa, L. / Lingford, J.P. / Razif, M.F.M. / Thore, S. / Rackham, O.
Funding support Switzerland, Australia, 9items
OrganizationGrant numberCountry
Swiss National Science Foundation316030-128787 Switzerland
Swiss National Science Foundation31003A_140924 Switzerland
Swiss National Science Foundation31003A_124909 Switzerland
Novartis Foundation for medical-biological research09A07 Switzerland
Australian Research CouncilFT0991008 Australia
Australian Research CouncilFT0991113 Australia
Australian Research CouncilDP140104111 Australia
National Health and Medical Research CouncilAPP1058442 Australia
National Health and Medical Research CouncilAPP1045677 Australia
CitationJournal: Nat Commun / Year: 2014
Title: An artificial PPR scaffold for programmable RNA recognition.
Authors: Coquille, S. / Filipovska, A. / Chia, T. / Rajappa, L. / Lingford, J.P. / Razif, M.F. / Thore, S. / Rackham, O.
History
DepositionOct 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.3Jan 10, 2024Group: 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
B: Pentatricopeptide repeat protein


Theoretical massNumber of molelcules
Total (without water)66,4502
Polymers66,4502
Non-polymers00
Water0
1
A: Pentatricopeptide repeat protein


Theoretical massNumber of molelcules
Total (without water)33,2251
Polymers33,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentatricopeptide repeat protein


Theoretical massNumber of molelcules
Total (without water)33,2251
Polymers33,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.720, 204.720, 204.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Pentatricopeptide repeat protein /


Mass: 33225.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 7.0, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.07253 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07253 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 6865 / % possible obs: 99.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23
Reflection shellResolution: 3.85→3.95 Å / Redundancy: 19.6 % / Rmerge(I) obs: 1.96 / Mean I/σ(I) obs: 2.18 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PJQ

4pjq


Resolution: 3.85→19.791 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 672 9.88 %
Rwork0.1786 --
obs0.1836 6801 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.85→19.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 0 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113250
X-RAY DIFFRACTIONf_angle_d1.3614374
X-RAY DIFFRACTIONf_dihedral_angle_d19.1241246
X-RAY DIFFRACTIONf_chiral_restr0.06528
X-RAY DIFFRACTIONf_plane_restr0.007550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8503-4.14510.38571360.28861215X-RAY DIFFRACTION100
4.1451-4.55760.2851310.20161226X-RAY DIFFRACTION100
4.5576-5.20660.24461370.1661204X-RAY DIFFRACTION100
5.2066-6.52060.27741340.25211222X-RAY DIFFRACTION100
6.5206-19.79130.17521340.14121262X-RAY DIFFRACTION100

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