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- PDB-6bv8: Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana co... -

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Basic information

Entry
Database: PDB / ID: 6bv8
TitleStructure of proteinaceous RNase P 1 (PRORP1) from A. thaliana complexed with Mn after 3-hour soak with juglone
ComponentsProteinaceous RNase P 1, chloroplastic/mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metallonuclease / PRORP / ribonuclease / PIN / tRNA processing / RNAse P / NYN domain / PPR domain / chloroplasts / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
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
5-hydroxynaphthalene-1,4-dione / : / Proteinaceous RNase P 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarasik, A. / Wu, N. / Fierke, C.A. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117141 United States
CitationJournal: To Be Published
Title: Inhibition of protein-only RNase P with Gambogic acid and Juglone
Authors: Wu, N. / Karasik, A. / Muehlbauer, L. / Koutmos, M. / Fierke, C.A.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.3Nov 6, 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: Proteinaceous RNase P 1, chloroplastic/mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0266
Polymers56,6611
Non-polymers3655
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-13 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.677, 111.332, 139.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 56660.734 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: PRORP1, At2g32230, F22D22.2 / Plasmid: Plasmid / Details (production host): pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta (DE3) / References: UniProt: Q66GI4, ribonuclease P

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-JUG / 5-hydroxynaphthalene-1,4-dione / Juglone


Mass: 174.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 18% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 2017
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.1→86.99 Å / Num. obs: 38500 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G23

4g23


Resolution: 2.1→86.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.741 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23608 1900 4.9 %RANDOM
Rwork0.2004 ---
obs0.20222 36554 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.091 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--1.78 Å20 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.1→86.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 17 236 4020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193877
X-RAY DIFFRACTIONr_bond_other_d0.0010.023749
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9575236
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0028550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76324.121182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6115698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8635.1481888
X-RAY DIFFRACTIONr_mcbond_other2.865.1461887
X-RAY DIFFRACTIONr_mcangle_it4.277.6992357
X-RAY DIFFRACTIONr_mcangle_other4.2697.7022358
X-RAY DIFFRACTIONr_scbond_it3.3455.4941989
X-RAY DIFFRACTIONr_scbond_other3.3455.4971976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2488.0712859
X-RAY DIFFRACTIONr_long_range_B_refined7.28659.8454531
X-RAY DIFFRACTIONr_long_range_B_other7.18459.9174423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 138 -
Rwork0.3 2603 -
obs--97.3 %

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