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- PDB-5izw: Crystal structure of RNA editing specific factor of designer PLS-... -

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Basic information

Entry
Database: PDB / ID: 5izw
TitleCrystal structure of RNA editing specific factor of designer PLS-type PPR-9R protein
ComponentsPLS9-PPR
KeywordsRNA BINDING PROTEIN / pentatricopeptide repeat / complex / MORF
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.738 Å
AuthorsYan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P.
CitationJournal: Nat Plants / Year: 2017
Title: MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing
Authors: Yan, J. / Zhang, Q. / Guan, Z. / Wang, Q. / Li, L. / Ruan, F. / Lin, R. / Zou, T. / Yin, P.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
A: PLS9-PPR
B: PLS9-PPR


Theoretical massNumber of molelcules
Total (without water)22,5342
Polymers22,5342
Non-polymers00
Water3,405189
1
A: PLS9-PPR


Theoretical massNumber of molelcules
Total (without water)11,2671
Polymers11,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PLS9-PPR


Theoretical massNumber of molelcules
Total (without water)11,2671
Polymers11,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.412, 67.412, 56.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PLS9-PPR


Mass: 11267.071 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Magnesium sulfate heptahydrate, 1,3-Bis[tris(hydroxymethyl)methylamino]propane, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.738→45 Å / Num. obs: 26305 / % possible obs: 99.9 % / Redundancy: 13.4 % / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data collection
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.738→36.501 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 1257 4.78 %
Rwork0.1755 --
obs0.1769 26272 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.738→36.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 189 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111596
X-RAY DIFFRACTIONf_angle_d1.1062140
X-RAY DIFFRACTIONf_dihedral_angle_d19.179602
X-RAY DIFFRACTIONf_chiral_restr0.338244
X-RAY DIFFRACTIONf_plane_restr0.005270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7383-1.80790.31551410.25762761X-RAY DIFFRACTION99
1.8079-1.89020.32051280.22122756X-RAY DIFFRACTION100
1.8902-1.98980.24631420.21142766X-RAY DIFFRACTION100
1.9898-2.11450.22291420.18852761X-RAY DIFFRACTION100
2.1145-2.27770.19371490.16512774X-RAY DIFFRACTION100
2.2777-2.50690.20611580.17932765X-RAY DIFFRACTION100
2.5069-2.86950.20291280.18142775X-RAY DIFFRACTION100
2.8695-3.61480.18621540.17262782X-RAY DIFFRACTION100
3.6148-36.50860.19981150.15682875X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.6247 Å / Origin y: 116.7232 Å / Origin z: 7.9213 Å
111213212223313233
T0.1822 Å2-0.0077 Å2-0.0194 Å2-0.1821 Å20.0208 Å2--0.2085 Å2
L0.4592 °2-0.2399 °2-0.1889 °2-0.4755 °20.276 °2--0.5989 °2
S-0.0045 Å °-0.0092 Å °0.0042 Å °0.0031 Å °-0.0042 Å °0.003 Å °-0.0163 Å °-0.0051 Å °-0.0089 Å °
Refinement TLS groupSelection details: all

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