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

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Basic information

Entry
Database: PDB / ID: 4xgl
TitleStructure of the nuclease subunit of human mitochondrial RNase P (MRPP3) at 1.8A
ComponentsMitochondrial ribonuclease P protein 3
KeywordsHYDROLASE / PPR domain / zinc binding domain / metallonuclease / RNase P
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 / SAD / Resolution: 1.8 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-2 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.250, 99.250, 50.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Detailsbiological unit is the same as asym.

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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.: 178 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: potassium citrate, PEG3350, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46217 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 34.14 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.097 / Χ2: 0.977 / Net I/σ(I): 12.89 / Num. measured all: 488725
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.850.4332.270.8936138340033932.38699.8
1.85-1.90.6411.6991.2636167332933291.784100
1.9-1.950.7631.2271.8234551320632041.28899.9
1.95-2.010.8380.9962.3133051309830961.04799.9
2.01-2.080.9120.7143.1331592301930190.751100
2.08-2.150.930.5463.9428393294829360.57899.6
2.15-2.230.9670.4155.630610283228310.436100
2.23-2.320.9820.3137.4129988274327430.329100
2.32-2.430.9880.2538.9528254260826080.265100
2.43-2.550.9920.20411.0127256251825180.215100
2.55-2.680.9930.16113.2824671236623660.169100
2.68-2.850.9960.12515.8822762227122710.132100
2.85-3.040.9970.10120.8623572210721070.106100
3.04-3.290.9980.07726.821752198419840.081100
3.29-3.60.9990.06232.0419656183318330.066100
3.6-4.030.9980.05135.9616142166216620.054100
4.03-4.650.9990.04641.9815686147414740.048100
4.65-5.690.9990.04543.3513434125112500.04799.9
5.69-8.050.9990.04440.2892629689680.047100
8.050.9980.03949.7957885675650.04199.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.625 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1609 3.48 %Random selection
Rwork0.1885 44578 --
obs0.1899 46187 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.3 Å2 / Biso mean: 61.5153 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 1.8→49.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 13 178 2985
Biso mean--85.68 50.79 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072889
X-RAY DIFFRACTIONf_angle_d0.923896
X-RAY DIFFRACTIONf_chiral_restr0.039429
X-RAY DIFFRACTIONf_plane_restr0.004494
X-RAY DIFFRACTIONf_dihedral_angle_d15.2581092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.85810.37671380.35539824120
1.8581-1.92450.35561490.308840474196
1.9245-2.00160.30111450.273740154160
2.0016-2.09270.27091450.232340314176
2.0927-2.2030.24651440.207340314175
2.203-2.34110.22351500.187240324182
2.3411-2.52180.22221450.185240444189
2.5218-2.77560.22061460.183540634209
2.7756-3.17710.22931450.184540834228
3.1771-4.00260.22611490.173940634212
4.0026-49.64380.20081530.168741874340
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)
12.4395-1.51850.83383.4042-1.21751.60480.0043-0.0135-0.25630.02530.2111-0.00890.11320.0013-0.21690.2084-0.0134-0.04520.2111-0.03250.261855.649132.698822.2789
20.3452-1.1668-0.61988.32553.4631.3734-0.13740.1038-0.1751-0.1571-0.07790.05220.1159-0.06050.18530.52010.045-0.0190.3869-0.07270.670970.20132.405918.6143
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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