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- PDB-6lvr: Crystal structure of the PPR domain of Arabidopsis thaliana prote... -

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Basic information

Entry
Database: PDB / ID: 6lvr
TitleCrystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA
Components
  • Proteinaceous RNase P 1, chloroplastic/mitochondrial
  • yeast phenylalanine tRNA
KeywordsRNA BINDING PROTEIN / Protein-only RNase P tRNA processing tRNA complex Pentatricopeptide repeat convergent evolution
Function / homology
Function and homology information


ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / chloroplast / mitochondrion / metal ion binding
Similarity search - Function
Protein-only RNase P, C-terminal / Protein-only RNase P / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Proteinaceous RNase P 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTeramoto, T. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA50165 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA.
Authors: Teramoto, T. / Kaitany, K.J. / Kakuta, Y. / Kimura, M. / Fierke, C.A. / Hall, T.M.T.
History
DepositionFeb 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Proteinaceous RNase P 1, chloroplastic/mitochondrial
A: Proteinaceous RNase P 1, chloroplastic/mitochondrial
D: yeast phenylalanine tRNA
B: yeast phenylalanine tRNA


Theoretical massNumber of molelcules
Total (without water)96,6664
Polymers96,6664
Non-polymers00
Water63135
1
C: Proteinaceous RNase P 1, chloroplastic/mitochondrial
D: yeast phenylalanine tRNA


Theoretical massNumber of molelcules
Total (without water)48,3332
Polymers48,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint5 kcal/mol
Surface area21270 Å2
MethodPISA
2
A: Proteinaceous RNase P 1, chloroplastic/mitochondrial
B: yeast phenylalanine tRNA


Theoretical massNumber of molelcules
Total (without water)48,3332
Polymers48,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-1 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.480, 131.701, 155.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Proteinaceous RNase P 1, chloroplastic/mitochondrial / Pentatricopeptide repeat-containing protein At2g32230


Mass: 23442.951 Da / Num. of mol.: 2 / Mutation: Y266N, F284Q, F291Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRORP1, At2g32230, F22D22.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66GI4, ribonuclease P
#2: RNA chain yeast phenylalanine tRNA


Mass: 24890.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsAuthors Substituted SASS for original EAATESSP sequence.

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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: 4.48 Å3/Da / Density % sol: 72.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.5 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 42492 / % possible obs: 99.9 % / Redundancy: 5 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.124 / Net I/σ(I): 13.8
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2074 / CC1/2: 0.792 / CC star: 0.94 / Rpim(I) all: 0.48 / Rrim(I) all: 1.075 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G24, 1EHZ

4g24

1ehz


Resolution: 2.85→49.312 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: FREE R-VALUE / ESU R Free: 0.295
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2554 2087 5.059 %
Rwork0.2347 --
all0.236 --
obs-41250 99.821 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 120.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.223 Å2-0 Å2-0 Å2
2---1.877 Å20 Å2
3---1.655 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 3136 0 35 6226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0136603
X-RAY DIFFRACTIONr_bond_other_d0.0280.0184454
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.6159626
X-RAY DIFFRACTIONr_angle_other_deg2.2492.07310507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3025383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57522.814167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87915592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.431522
X-RAY DIFFRACTIONr_chiral_restr0.1240.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.025155
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021311
X-RAY DIFFRACTIONr_nbd_refined0.1750.21240
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2570.24608
X-RAY DIFFRACTIONr_nbtor_refined0.2090.22864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.222
X-RAY DIFFRACTIONr_nbd_other0.2320.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.260.22
X-RAY DIFFRACTIONr_mcbond_it1.1377.1361544
X-RAY DIFFRACTIONr_mcbond_other1.1927.1351543
X-RAY DIFFRACTIONr_mcangle_it1.91810.6831923
X-RAY DIFFRACTIONr_mcangle_other1.95210.6851924
X-RAY DIFFRACTIONr_scbond_it1.81816.2965059
X-RAY DIFFRACTIONr_scbond_other2.08116.2945058
X-RAY DIFFRACTIONr_scangle_it3.06824.5997703
X-RAY DIFFRACTIONr_scangle_other3.06724.5997703
X-RAY DIFFRACTIONr_lrange_it4.41146.0598463
X-RAY DIFFRACTIONr_lrange_other4.463146.0648464
X-RAY DIFFRACTIONr_rigid_bond_restr15.104311057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.3861480.3572854X-RAY DIFFRACTION100
2.924-3.0040.3611470.3382802X-RAY DIFFRACTION100
3.004-3.0910.3331470.3112683X-RAY DIFFRACTION100
3.091-3.1860.2981230.2822660X-RAY DIFFRACTION100
3.186-3.2910.2751460.252574X-RAY DIFFRACTION100
3.291-3.4060.2591250.2352466X-RAY DIFFRACTION100
3.406-3.5350.2541420.2312376X-RAY DIFFRACTION99.881
3.535-3.6790.2371200.232307X-RAY DIFFRACTION99.9177
3.679-3.8420.2811190.2282214X-RAY DIFFRACTION99.9143
3.842-4.030.2421310.2222093X-RAY DIFFRACTION99.597
4.03-4.2480.2221140.1842028X-RAY DIFFRACTION99.9533
4.248-4.5050.215920.1821906X-RAY DIFFRACTION100
4.505-4.8160.1971010.1941790X-RAY DIFFRACTION99.7363
4.816-5.2010.258850.2361721X-RAY DIFFRACTION100
5.201-5.6970.269860.241552X-RAY DIFFRACTION100
5.697-6.3680.298660.2551433X-RAY DIFFRACTION100
6.368-7.3520.255580.2361281X-RAY DIFFRACTION100
7.352-8.9990.236520.2071087X-RAY DIFFRACTION100
8.999-12.7050.209530.2855X-RAY DIFFRACTION99.6707
12.705-49.3120.287310.305471X-RAY DIFFRACTION91.1071

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