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- PDB-4m59: Crystal structure of the pentatricopeptide repeat protein PPR10 i... -

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Basic information

Entry
Database: PDB / ID: 4m59
TitleCrystal structure of the pentatricopeptide repeat protein PPR10 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: 2.46 Å
AuthorsYin, P. / Li, Q. / Yan, C. / Liu, Y. / Yan, N.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the modular recognition of single-stranded RNA by PPR proteins.
Authors: Yin, P. / Li, Q. / Yan, C. / Liu, Y. / Liu, J. / Yu, F. / Wang, Z. / Long, J. / He, J. / Wang, H.W. / Wang, J. / Zhu, J.K. / Shi, Y. / Yan, N.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)169,8575
Polymers169,7624
Non-polymers951
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
ΔGint-73 kcal/mol
Surface area62850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.428, 83.428, 226.913
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: 79285.609 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 / Details: This RNA oligo is synthesized by TAKARA company.
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG 3350, 8% Tacsimate, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9067 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9067 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. all: 56165 / Num. obs: 54087 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.45→2.54 Å / % possible all: 98

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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: PDB ENTRY 4M57

4m57


Resolution: 2.46→39.87 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 2744 5.08 %
Rwork0.26 --
obs0.261 54006 96.2 %
all-56121 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.81 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1831 Å20 Å2-0 Å2
2--0.1831 Å2-0 Å2
3----2.8848 Å2
Refinement stepCycle: LAST / Resolution: 2.46→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10381 647 5 114 11147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511286
X-RAY DIFFRACTIONf_angle_d0.99915430
X-RAY DIFFRACTIONf_dihedral_angle_d18.3724156
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 (%)
2.4576-2.50.40211370.39772572X-RAY DIFFRACTION98
2.5-2.54540.43131230.39822612X-RAY DIFFRACTION98
2.5454-2.59440.37191300.38682641X-RAY DIFFRACTION98
2.5944-2.64730.38641390.39272550X-RAY DIFFRACTION98
2.6473-2.70490.3971390.37152613X-RAY DIFFRACTION98
2.7049-2.76780.37221410.37142603X-RAY DIFFRACTION97
2.7678-2.8370.37191200.3622584X-RAY DIFFRACTION97
2.837-2.91370.3961590.35592554X-RAY DIFFRACTION97
2.9137-2.99940.36211390.32952597X-RAY DIFFRACTION97
2.9994-3.09620.32941490.32362554X-RAY DIFFRACTION96
3.0962-3.20680.32661680.31962518X-RAY DIFFRACTION96
3.2068-3.33510.33541310.30442583X-RAY DIFFRACTION96
3.3351-3.48680.29711340.28472486X-RAY DIFFRACTION95
3.4868-3.67050.23171290.25462514X-RAY DIFFRACTION94
3.6705-3.90030.21721480.23962493X-RAY DIFFRACTION93
3.9003-4.20120.24891390.21042465X-RAY DIFFRACTION92
4.2012-4.62340.24031280.19972410X-RAY DIFFRACTION91
4.6234-5.29110.23481350.21672512X-RAY DIFFRACTION94
5.2911-6.66110.2921440.27522673X-RAY DIFFRACTION100
6.6611-39.87120.28631120.2132728X-RAY DIFFRACTION99
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)
13.9442-0.6898-2.54153.14852.57924.98690.05230.01030.5480.16390.1522-0.0526-0.1557-0.2564-0.18880.29140.0875-0.08250.54530.06030.4279-33.408964.4765-14.1033
22.36410.26641.11870.6071-0.7442.8481-0.05910.08020.10390.20710.01430.3258-0.00060.14440.10.39750.1214-0.0240.4993-0.0850.552218.15461.6869-7.9505
31.20190.10711.29523.0332.18054.32930.39250.0332-0.64750.03760.08610.3210.47520.2717-0.43050.49380.1481-0.16680.8405-0.04830.71669.268822.74036.6413
40.76580.37070.64161.67121.83626.7562-0.1564-0.0651-0.10080.33920.060.07550.29690.05290.09350.36330.06830.01990.44340.03690.287635.496641.0835-2.5171
51.7161-0.2288-0.5336.71993.49683.2106-0.242-0.11550.0464-0.11140.2859-0.2991-0.3049-0.1534-0.03220.43110.1787-0.08440.72060.00610.412-16.403247.6207-1.9631
61.9095-2.05840.33543.32241.1064.29290.18070.25050.168-0.1125-0.1184-0.3168-0.5684-0.0228-0.07350.41830.0371-0.12020.5672-0.04221.0406-6.882885.7278-19.5306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 74:277 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 348:548 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 595:748 )
4X-RAY DIFFRACTION4(CHAIN B AND RESID 72:277 )
5X-RAY DIFFRACTION5(CHAIN B AND RESID 350:548 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 595:748 )

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