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- PDB-4g25: Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. tha... -

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Basic information

Entry
Database: PDB / ID: 4g25
TitleCrystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr
ComponentsPentatricopeptide repeat-containing protein At2g32230, mitochondrial
KeywordsRNA BINDING PROTEIN / Metallonuclease / PRORP / Ribonuclease / PIN / tRNA processing / Rnase P / NYN domain / PPR domain / Chloroplasts
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 / Rossmann fold - #11980 / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Protein-only RNase P, C-terminal / Protein-only RNase P / Rossmann fold - #11980 / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STRONTIUM ION / Proteinaceous RNase P 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoutmos, M. / Howard, M.J. / Fierke, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.
Authors: Howard, M.J. / Lim, W.H. / Fierke, C.A. / Koutmos, M.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentatricopeptide repeat-containing protein At2g32230, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4703
Polymers57,3171
Non-polymers1532
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.844, 111.814, 140.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pentatricopeptide repeat-containing protein At2g32230, mitochondrial


Mass: 57317.258 Da / Num. of mol.: 1 / Fragment: UNP residues 77-572
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g32230, F22D22.2 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q66GI4, ribonuclease P
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 57.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3,350, 0.1 M sodium citrate pH 5.5, and 0.02 M SrCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2012
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 45501 / Num. obs: 44773 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4456 / Rsym value: 0.63 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G23

4g23


Resolution: 2→33.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.696 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23354 2269 5.1 %RANDOM
Rwork0.19405 ---
obs0.19606 42464 98.4 %-
all-44733 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--1.6 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 2 235 4024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193924
X-RAY DIFFRACTIONr_bond_other_d0.0010.023823
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9635312
X-RAY DIFFRACTIONr_angle_other_deg1.1283.0028716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48324.127189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58915670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6971530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 150 -
Rwork0.251 2827 -
obs--97.54 %

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