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- PDB-8ssf: Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter... -

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Basic information

Entry
Database: PDB / ID: 8ssf
TitleMinimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus
ComponentsRNA-free ribonuclease P
KeywordsHYDROLASE / RNA-free ribonuclease P / Nuclease / RNA Binding Protein
Function / homologyRNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / RNA-free ribonuclease P
Function and homology information
Biological speciesHydrogenobacter thermophilus TK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMendoza, J. / Mallik, L. / Wilhelm, C.A. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)117141 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P.
Authors: Wilhelm, C.A. / Mallik, L. / Kelly, A.L. / Brotzman, S. / Mendoza, J. / Anders, A.G. / Leskaj, S. / Castillo, C. / Ruotolo, B.T. / Cianfrocco, M.A. / Koutmos, M.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2545
Polymers44,9662
Non-polymers2883
Water75742
1
A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
hetero molecules

A: RNA-free ribonuclease P
B: RNA-free ribonuclease P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,50710
Polymers89,9314
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9890 Å2
ΔGint-153 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.579, 109.214, 106.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein RNA-free ribonuclease P / RNA-free RNase P / Protein-only RNase P


Mass: 22482.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus TK-6 (bacteria)
Gene: HTH_1307 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DIV8, ribonuclease P
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2020
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.5→69.72 Å / Num. obs: 18589 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.111 / Rrim(I) all: 0.324 / Χ2: 0.84 / Net I/σ(I): 6.3 / Num. measured all: 159064
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 4.001 / Num. measured all: 18292 / Num. unique obs: 2076 / CC1/2: 0.434 / Rpim(I) all: 1.443 / Rrim(I) all: 4.26 / Χ2: 0.73 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F3E

7f3e


Resolution: 2.5→69.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.139 / SU ML: 0.256 / Cross valid method: FREE R-VALUE / ESU R: 0.365 / ESU R Free: 0.255
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.244 964 5.193 %
Rwork0.2 --
obs-18563 100 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 70.31 Å2
Baniso -1Baniso -2Baniso -3
1-5.538 Å20 Å20 Å2
2---0.474 Å20 Å2
3----5.063 Å2
Refinement stepCycle: LAST / Resolution: 2.5→69.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 15 42 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162853
X-RAY DIFFRACTIONr_angle_refined_deg1.91.6454021
X-RAY DIFFRACTIONr_angle_other_deg0.571.5696554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3865350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.306526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9910539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02710
X-RAY DIFFRACTIONr_nbd_refined0.2140.2579
X-RAY DIFFRACTIONr_nbd_other0.2260.264
X-RAY DIFFRACTIONr_nbtor_refined0.180.21434
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.236
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_it9.0976.261406
X-RAY DIFFRACTIONr_mcbond_other9.0896.2591406
X-RAY DIFFRACTIONr_mcangle_it11.46711.2981751
X-RAY DIFFRACTIONr_mcangle_other11.46711.3011752
X-RAY DIFFRACTIONr_scbond_it13.2317.6531571
X-RAY DIFFRACTIONr_scbond_other13.2127.6441560
X-RAY DIFFRACTIONr_scangle_it18.36513.5062269
X-RAY DIFFRACTIONr_scangle_other18.31113.4832252
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 81 -
Rwork0.359 1269 -
obs--99.93 %

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