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- PDB-6d1r: Structure of Staphylococcus aureus RNase P protein at 2.0 angstrom -

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Basic information

Entry
Database: PDB / ID: 6d1r
TitleStructure of Staphylococcus aureus RNase P protein at 2.0 angstrom
ComponentsRibonuclease P protein component
KeywordsRNA BINDING PROTEIN / RNase / P protein / tRNA processing / RNA metabolism
Function / homology
Function and homology information


ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.995 Å
AuthorsHa, L. / Colquhoun, J. / Noinaj, N. / Das, C. / Dunman, P. / Flaherty, D.P.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus.
Authors: Ha, L. / Colquhoun, J. / Noinaj, N. / Das, C. / Dunman, P.M. / Flaherty, D.P.
History
DepositionApr 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 13, 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: Ribonuclease P protein component


Theoretical massNumber of molelcules
Total (without water)13,8291
Polymers13,8291
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.159, 72.159, 58.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

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Components

#1: Protein Ribonuclease P protein component / / RNaseP protein / Protein C5


Mass: 13829.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: rnpA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A0H5, ribonuclease P
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 3.3M (NH4)2SO4, 0.15M potassium phosphate pH6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12313 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Χ2: 1.195 / Net I/σ(I): 7.3 / Num. measured all: 111835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.079.41.21612140.6250.4181.2871.359100
2.07-2.158.90.94311960.7260.3351.0011.266100
2.15-2.258.80.69112030.8610.2470.7351.184100
2.25-2.378.90.50912110.9160.180.5411.172100
2.37-2.529.60.36612400.9610.1230.3861.019100
2.52-2.719.60.24412120.9810.0830.2580.96499.9
2.71-2.9990.1412310.9930.0490.1480.916100
2.99-3.428.60.07112310.9980.0260.0761.116100
3.42-4.319.60.04612560.9990.0160.0491.402100
4.31-508.60.03913190.9980.0140.0421.54399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å29.41 Å
Translation3 Å29.41 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→31.246 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1223 9.94 %
Rwork0.2141 11086 -
obs0.2161 12309 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.48 Å2 / Biso mean: 59.7886 Å2 / Biso min: 29.28 Å2
Refinement stepCycle: final / Resolution: 1.995→31.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 36 904
Biso mean---49.03 -
Num. residues----109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9954-2.07530.3431230.32371125124891
2.0753-2.16970.3151360.26712251361100
2.1697-2.2840.26521400.239912181358100
2.284-2.42710.23331350.225812111346100
2.4271-2.61440.23681370.219712311368100
2.6144-2.87730.26521350.22212471382100
2.8773-3.29330.23121350.221412551390100
3.2933-4.14770.20351330.194812511384100
4.1477-31.24960.22651490.199513231472100
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)
14.2640.04370.89455.8124-0.3544.89290.1570.458-0.6207-0.6166-0.1432-0.23051.45230.56870.09350.58220.2045-0.05070.4445-0.02960.375813.361818.90914.9603
23.5267-0.5377-3.51353.1290.5994.39870.03660.2846-0.2383-0.2744-0.06780.36650.2265-0.17720.00690.33620.0278-0.05720.25370.0040.31372.130430.067515.1084
34.0267-0.2734-1.56935.68160.01036.27090.0443-0.06470.132-0.0732-0.0162-0.4153-0.02460.7068-0.04820.29120.0333-0.0390.4397-0.00310.281712.876930.204919.9359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 48 )A5 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 72 )A49 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 113 )A73 - 113

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