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- PDB-4pjq: Crystal structure of designed cPPR-polyG protein -

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Basic information

Entry
Database: PDB / ID: 4pjq
TitleCrystal structure of designed cPPR-polyG protein
ComponentsPentatricopeptide repeat protein
KeywordsDE NOVO PROTEIN / RNA BINDING PROTEIN / designer RNA-binding proteins / pentatricopeptide repeat / synthetic biology / RNA-protein interactions
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.353 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 Council (ARC)FT0991008 Australia
Australian Research Council (ARC)FT0991113 Australia
Australian Research Council (ARC)DP140104111 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058442 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1045677 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
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: pdbx_audit_support / pdbx_database_status ...pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible ..._pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
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)65,7162
Polymers65,7162
Non-polymers00
Water0
1
A: Pentatricopeptide repeat protein


Theoretical massNumber of molelcules
Total (without water)32,8581
Polymers32,8581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentatricopeptide repeat protein


Theoretical massNumber of molelcules
Total (without water)32,8581
Polymers32,8581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.543, 207.543, 207.543
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: 32857.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 0.1M BisTris pH 6.7, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→47.614 Å / Num. obs: 20728 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.8
Reflection shellResolution: 3.35→3.62 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
Aimlessdata scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PJS

4pjs


Resolution: 3.353→47.614 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 2065 9.96 %Random selection
Rwork0.1902 ---
obs0.1956 20728 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.353→47.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 0 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033250
X-RAY DIFFRACTIONf_angle_d0.6854374
X-RAY DIFFRACTIONf_dihedral_angle_d16.3031246
X-RAY DIFFRACTIONf_chiral_restr0.05528
X-RAY DIFFRACTIONf_plane_restr0.003550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3527-3.43070.39071380.35551230X-RAY DIFFRACTION100
3.4307-3.51640.40391440.37311238X-RAY DIFFRACTION100
3.5164-3.61150.32531410.31521228X-RAY DIFFRACTION100
3.6115-3.71770.3651400.29781246X-RAY DIFFRACTION100
3.7177-3.83770.33171340.2661262X-RAY DIFFRACTION100
3.8377-3.97480.27651390.25621249X-RAY DIFFRACTION99
3.9748-4.13380.25781360.19791218X-RAY DIFFRACTION100
4.1338-4.32180.2431400.18771290X-RAY DIFFRACTION100
4.3218-4.54950.23451380.15831226X-RAY DIFFRACTION100
4.5495-4.83430.1711340.13351238X-RAY DIFFRACTION100
4.8343-5.20710.21841420.14841241X-RAY DIFFRACTION100
5.2071-5.73040.20261350.18481247X-RAY DIFFRACTION100
5.7304-6.55770.29951380.22711244X-RAY DIFFRACTION100
6.5577-8.25510.281360.17891254X-RAY DIFFRACTION100
8.2551-47.61840.20621300.15691252X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.0151 Å / Origin y: -2.0535 Å / Origin z: -52.9036 Å
111213212223313233
T0.9632 Å20.0155 Å2-0.0414 Å2-0.8446 Å20.0645 Å2--0.8903 Å2
L0.9799 °20.1152 °2-0.344 °2--0.177 °20.8875 °2--1.3787 °2
S-0.2348 Å °0.1474 Å °0.0884 Å °0.0353 Å °0.0257 Å °-0.0503 Å °-0.0091 Å °0.0458 Å °0 Å °
Refinement TLS groupSelection details: all

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