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- PDB-4xgm: Structure of the nuclease subunit of human mitochondrial RNase P ... -

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Basic information

Entry
Database: PDB / ID: 4xgm
TitleStructure of the nuclease subunit of human mitochondrial RNase P (MRPP3) at 1.98A
ComponentsMitochondrial ribonuclease P protein 3
KeywordsHYDROLASE / PPR domain / zinc binding domain / metallonuclease / RNase P / mitochondria
Function / homology
Function and homology information


rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / tRNA modification in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mitochondrial nucleoid / mitochondrial matrix ...rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / tRNA modification in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mitochondrial nucleoid / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding
Similarity search - Function
Mitochondrial ribonuclease P catalytic subunit / Protein-only RNase P, C-terminal / Protein-only RNase P / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Mitochondrial ribonuclease P catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsReinhard, L. / Sridhara, S. / Hallberg, B.M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2011-6510 Sweden
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure of the nuclease subunit of human mitochondrial RNase P.
Authors: Reinhard, L. / Sridhara, S. / Hallberg, B.M.
History
DepositionDec 31, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial ribonuclease P protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3704
Polymers44,1211
Non-polymers2503
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-2 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.040, 99.040, 50.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Mitochondrial ribonuclease P protein 3 / Mitochondrial RNase P protein 3


Mass: 44120.523 Da / Num. of mol.: 1 / Fragment: UNP residues 207-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0391, MRPP3 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: O15091, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, PEG 6000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.98→45.067 Å / Num. obs: 34479 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.99 Å2 / Rmerge(I) obs: 0.093 / Χ2: 0.974 / Net I/σ(I): 16.54
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.98-2.0370.4772.025117938255325512.18799.9
2.03-2.090.6721.4951.3517198245524551.616100
2.09-2.150.7351.161.7516668240424021.25499.9
2.15-2.210.8530.8372.4415845231923170.90699.9
2.21-2.290.9160.623.2214911225822570.673100
2.29-2.370.9470.4554.1914267222022200.496100
2.37-2.460.9760.3655.3314350208620850.395100
2.46-2.560.9840.2757.0914273202320230.298100
2.56-2.670.9890.2039.0913858197219720.219100
2.67-2.80.9940.15611.5612974186818680.169100
2.8-2.950.9960.11415.2111834177017690.12499.9
2.95-3.130.9970.07920.2610774167816760.08699.9
3.13-3.350.9990.05728.4211395159915990.062100
3.35-3.620.9990.04235.8710560148714870.046100
3.62-3.960.9990.03245.739376136313630.035100
3.96-4.430.9990.02851.87839123412330.03199.9
4.43-5.110.9990.02756.57304109010900.029100
5.11-6.260.9990.02855.765029429420.031100
6.26-8.860.9990.02559.5645067327310.02899.9
8.8610.02169.6825674274210.02398.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xgl

4xgl


Resolution: 1.98→45.067 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1205 3.5 %Random selection
Rwork0.1929 33244 --
obs0.194 34449 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.57 Å2 / Biso mean: 63.5861 Å2 / Biso min: 18.32 Å2
Refinement stepCycle: final / Resolution: 1.98→45.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 13 149 2948
Biso mean--72.09 50 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082851
X-RAY DIFFRACTIONf_angle_d0.9573838
X-RAY DIFFRACTIONf_chiral_restr0.039424
X-RAY DIFFRACTIONf_plane_restr0.005484
X-RAY DIFFRACTIONf_dihedral_angle_d14.7761070
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9801-2.05940.32331330.331736763809
2.0594-2.15310.30171320.278536583790
2.1531-2.26660.23151360.226836503786
2.2666-2.40860.26221350.2136853820
2.4086-2.59450.21761320.194236613793
2.5945-2.85560.22841310.189737003831
2.8556-3.26870.24731320.194536923824
3.2687-4.11780.21491370.172137313868
4.1178-45.07850.19731370.169837913928
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)
12.314-1.68710.64723.8819-1.33761.32180.0143-0.0018-0.38830.06590.2605-0.00980.15320.0405-0.2690.2473-0-0.11170.2364-0.02810.312755.478932.503521.9708
2-0.0402-0.9449-0.08288.69453.23950.7861-0.12720.1774-0.069-0.3288-0.0995-0.12940.0937-0.06660.19380.58650.046-0.05830.4558-0.12870.820969.82722.212918.0474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 341 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 582 )A0

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