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- PDB-4oe1: Crystal structure of the pentatricopeptide repeat protein PPR10 (... -

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Basic information

Entry
Database: PDB / ID: 4oe1
TitleCrystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt PSAJ rna element
Components
  • Chloroplast pentatricopeptide repeat protein 10
  • psaJ RNA
KeywordsRNA BINDING PROTEIN/RNA / PENTATRICOPEPTIDE REPEATS / SUPERHELICAL / RNA BINDING PROTEIN / RNA / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


mRNA stabilization / chloroplast stroma / mRNA processing / mRNA binding / identical protein binding
Similarity search - Function
PPR repeat / PPR repeat / PPR repeat family / Pentatricopeptide repeat domain / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Pentatricopeptide repeat-containing protein 10, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, Q. / Yan, C. / Wu, J. / Yin, P. / Yan, N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Examination of the dimerization states of the single-stranded RNA recognition protein pentatricopeptide repeat 10 (PPR10).
Authors: Li, Q. / Yan, C. / Xu, H. / Wang, Z. / Long, J. / Li, W. / Wu, J. / Yin, P. / Yan, N.
History
DepositionJan 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloroplast pentatricopeptide repeat protein 10
B: Chloroplast pentatricopeptide repeat protein 10
D: psaJ RNA
C: psaJ RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,8895
Polymers169,7944
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-73 kcal/mol
Surface area62800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.318, 83.318, 225.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Chloroplast pentatricopeptide repeat protein 10 / Pentatricopeptide repeat10


Mass: 79301.672 Da / Num. of mol.: 2 / Fragment: UNP residues 69-786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ppr10, ZEAMMB73_867042 / Production host: Escherichia coli (E. coli) / References: UniProt: B8Y6I0
#2: RNA chain psaJ RNA


Mass: 5595.259 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 9% PEG 3350, 0.1M MES 5.5, 6% Tacsimate, pH 6.0, 70 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 37816 / Num. obs: 37060 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M59

4m59


Resolution: 2.8→34.259 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1855 5.01 %random
Rwork0.2629 ---
obs0.2636 37060 98.15 %-
all-37816 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.44 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4672 Å2-0 Å20 Å2
2---1.4672 Å20 Å2
3---2.9645 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10381 647 5 0 11033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511286
X-RAY DIFFRACTIONf_angle_d0.99915430
X-RAY DIFFRACTIONf_dihedral_angle_d18.3874156
X-RAY DIFFRACTIONf_chiral_restr0.071803
X-RAY DIFFRACTIONf_plane_restr0.0061867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87360.43131440.39882763X-RAY DIFFRACTION99
2.8736-2.95810.38711370.36752732X-RAY DIFFRACTION99
2.9581-3.05360.42871420.35942711X-RAY DIFFRACTION99
3.0536-3.16260.37511500.34962709X-RAY DIFFRACTION99
3.1626-3.28920.33581400.33182732X-RAY DIFFRACTION99
3.2892-3.43870.32641520.30972734X-RAY DIFFRACTION99
3.4387-3.61980.30171480.28032720X-RAY DIFFRACTION99
3.6198-3.84630.26611610.26082678X-RAY DIFFRACTION99
3.8463-4.14290.26371190.23082750X-RAY DIFFRACTION98
4.1429-4.55890.1911380.21172686X-RAY DIFFRACTION98
4.5589-5.21660.23861400.222698X-RAY DIFFRACTION97
5.2166-6.56480.28851400.27592678X-RAY DIFFRACTION97
6.5648-34.26170.24171440.22572614X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 95.3906 Å / Origin y: 40.5851 Å / Origin z: -8.9344 Å
111213212223313233
T0.5186 Å2-0.0769 Å2-0.1169 Å2-0.3724 Å20.075 Å2--0.4122 Å2
L-0.0655 °2-0.1684 °2-0.1003 °2-0.5711 °2-0.0165 °2--0.1629 °2
S0.0386 Å °-0.0739 Å °-0.019 Å °0.0324 Å °-0.0768 Å °-0.026 Å °-0.0148 Å °0.0298 Å °0.0355 Å °
Refinement TLS groupSelection details: all

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