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- PDB-9ept: Crystal structure of the Plastid Redox Insensitive 2 from Arabido... -

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Basic information

Entry
Database: PDB / ID: 9ept
TitleCrystal structure of the Plastid Redox Insensitive 2 from Arabidopsis thaliana
ComponentsProtein PLASTID REDOX INSENSITIVE 2, chloroplastic
KeywordsTRANSCRIPTION / Plastid-encoded RNA-polymerase / Redox / Arabidopsis thaliana
Function / homologyProtein PLASTID REDOX INSENSITIVE 2 / plastid nucleoid / plastid-encoded plastid RNA polymerase complex / chloroplast nucleoid / response to light intensity / regulation of gene expression / DNA binding / Protein PLASTID REDOX INSENSITIVE 2, chloroplastic
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsRuedas, R. / Vallet, A. / Blanvillain, R. / Cobessi, D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0031 France
CitationJournal: To Be Published
Title: Crystal structure of the Plastid Redox Insensitive 2 from Arabidopsis thaliana
Authors: Ruedas, R. / Vallet, A. / Blanvillain, R. / Cobessi, D.
History
DepositionMar 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PLASTID REDOX INSENSITIVE 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0662
Polymers12,9731
Non-polymers921
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area7040 Å2
Unit cell
Length a, b, c (Å)37.270, 37.270, 101.000
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 Protein PLASTID REDOX INSENSITIVE 2, chloroplastic


Mass: 12973.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRIN2, At1g10522, T10O24.14 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XIK0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 6% PEG 8K, 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 25% glycerol, protein concentration of 15 mg/mL.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.74→37.27 Å / Num. obs: 14084 / % possible obs: 99.8 % / Redundancy: 10.91 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.55
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 8.91 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 1041 / CC1/2: 0.927 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.743→37.27 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 733 5.22 %
Rwork0.1694 --
obs0.1715 14038 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.743→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 6 77 996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005957
X-RAY DIFFRACTIONf_angle_d0.7691299
X-RAY DIFFRACTIONf_dihedral_angle_d9.174571
X-RAY DIFFRACTIONf_chiral_restr0.047136
X-RAY DIFFRACTIONf_plane_restr0.006172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.743-1.87760.23161420.20032657X-RAY DIFFRACTION99
1.8776-2.06660.23911620.18822631X-RAY DIFFRACTION100
2.0666-2.36550.20731570.17322648X-RAY DIFFRACTION100
2.3655-2.98010.2251260.19142686X-RAY DIFFRACTION100
2.9801-37.270.20231460.15482683X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3844-0.9449-1.19032.7944.08746.5272-0.02130.1025-0.0338-0.2244-0.22050.1866-0.3735-0.18650.20810.40170.0327-0.02530.2910.02110.34214.15699.9541-8.7429
22.85982.0847-2.71764.4767-3.90243.82470.3837-0.23340.23060.555-0.17280.3513-1.24790.1727-0.36930.4419-0.0240.00650.2886-0.03590.32260.528117.942521.0695
32.98220.5124-0.58642.724-1.38935.9636-0.039-0.220.1807-0.10290.0431-0.0165-0.20550.0730.01710.2442-0.0042-0.00790.1892-0.03760.27752.353810.938514.118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 114 )

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