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- PDB-6ov1: Structure of Staphylococcus aureus RNase P protein mutant with de... -

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Basic information

Entry
Database: PDB / ID: 6ov1
TitleStructure of Staphylococcus aureus RNase P protein mutant with defective mRNA degradation activity
ComponentsRibonuclease P protein component
KeywordsRNA BINDING PROTEIN / RNase P protein / tRNA processing / mRNA degradation
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / ribonuclease P complex / 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-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Ribonuclease P protein component
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHa, L. / Colquhoun, J. / Noinaj, N. / Das, C. / Dunman, P. / Flaherty, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI13468502 United States
CitationJournal: To Be Published
Title: Genetic and biochemical characterization of Staphylococcus aureus RnpA
Authors: Colquhoun, J.M. / Ha, L. / Noinaj, N. / Das, C. / Flaherty, D.P. / Dunman, P.M.
History
DepositionMay 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease P protein component
B: Ribonuclease P protein component


Theoretical massNumber of molelcules
Total (without water)31,8132
Polymers31,8132
Non-polymers00
Water2,270126
1
A: Ribonuclease P protein component


Theoretical massNumber of molelcules
Total (without water)15,9071
Polymers15,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease P protein component


Theoretical massNumber of molelcules
Total (without water)15,9071
Polymers15,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.386, 43.467, 45.837
Angle α, β, γ (deg.)91.110, 114.830, 110.950
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15906.618 Da / Num. of mol.: 2 / Mutation: P89A
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.: 126 / 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: 2.31 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Imidazole-HCl, pH8 1.3 M Sodium Citrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 1.657→50 Å / Num. obs: 29214 / % possible obs: 95.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 26.52 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.059 / Χ2: 1 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.66-1.721.80.51328380.5730.5130.7251.0492.2
1.72-1.791.80.38929000.6710.3880.550.9394.5
1.79-1.871.80.26229120.8210.2620.3710.98394.4
1.87-1.971.70.15929020.9350.1590.2250.96495.2
1.97-2.091.90.11429160.9610.1140.1621.0494.6
2.09-2.251.80.08229190.9760.0820.1151.04595.5
2.25-2.481.80.06629230.9810.0660.0941.12695.3
2.48-2.841.80.05129350.9890.0510.0721.06496.4
2.84-3.581.80.03729860.9920.0370.0521.02397.1
3.58-501.80.02729830.9960.0270.0380.79297.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D6T

1d6t


Resolution: 1.66→40.761 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2384 2003 6.86 %
Rwork0.1869 --
obs0.1905 29206 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 272.34 Å2 / Biso mean: 47.7669 Å2 / Biso min: 17.07 Å2
Refinement stepCycle: final / Resolution: 1.66→40.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 0 126 2024
Biso mean---43.7 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.66-1.69850.32241350.3086177987
1.6985-1.74440.33861320.2849195794
1.7444-1.79580.34211410.274191795
1.7958-1.85370.28361490.2538193695
1.8537-1.920.271420.2334195495
1.92-1.99680.25741480.2138192695
1.9968-2.08770.24911360.1948196295
2.0877-2.19780.21381530.1895191995
2.1978-2.33550.26511350.1877197796
2.3355-2.51580.24011450.189194395
2.5158-2.76890.22911480.2015197496
2.7689-3.16940.25251440.2025199597
3.1694-3.99260.25581440.1642198997
3.9926-40.7610.18831510.1522197597
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)
13.4305-4.6554-3.50117.29253.9817.846-0.2375-0.1728-0.14020.37460.25760.19220.3451-0.11980.01290.2466-0.0094-0.04520.24270.02710.18124.04197.987720.0265
23.50980.0102-3.41029.66531.25783.688-0.3699-0.1912-0.4564-0.08540.2596-0.27070.89890.45180.20190.30910.0267-0.05830.2844-0.00360.31613.9253.32918.1782
30.91170.9170.74727.78947.77337.6834-0.10230.0444-0.21420.4405-0.01950.20040.5195-0.0980.16460.29980.01330.00490.2856-0.02320.3049-14.4829-10.063-12.437
46.05714.88135.15234.22665.29278.8574-0.27480.05420.3386-0.3697-0.00970.4092-0.6916-0.40860.32040.28210.0499-0.04390.20840.05040.254-9.055711.1281-7.2176
54.4958-4.12356.2748.6056-3.95839.7609-0.3164-0.50530.10890.21130.124-0.0747-0.1695-0.03520.21560.2215-0.063-0.03980.185-0.03230.15622.45977.63474.7121
68.53573.57152.79465.28762.13585.6316-0.0595-0.26760.5760.2351-0.25280.6418-0.0797-0.56170.29870.22570.03310.01250.2461-0.02470.1684-11.34195.5277-0.1734
73.5771-4.6847-3.54136.36363.4826.68770.70721.05760.8836-0.49040.0121-0.7434-0.63270.5201-0.49490.2423-0.01940.01970.41360.02320.21632.45783.4396-8.689
82.6153.04180.47474.04-0.32689.1414-0.33770.9664-0.1845-0.08410.40160.11850.7086-0.38980.03480.24790.0149-0.04330.3169-0.05930.28611.8905-4.8588-6.6613
96.61363.0177-2.63747.0892-1.23033.21990.0456-0.6843-0.36830.4329-0.27180.08940.36860.06830.16430.3453-0.0186-0.01430.27780.00870.1644-7.93730.2151.5248
106.43-4.2718-1.46215.23615.00987.1408-0.0423-0.1565-0.1867-0.04640.165-0.25680.11160.5261-0.27680.2385-0.02030.00430.3123-0.03110.233111.9290.5666-1.2316
114.7559-4.1727-5.09254.14494.49768.2644-0.3444-0.053-0.01820.3190.028-0.02990.6548-0.26080.31350.3103-0.0484-0.05570.24490.0380.26130.9349-2.40585.9386
127.38053.55072.98914.47796.24759.7055-0.2021-0.44990.16050.1907-0.25260.27930.4336-0.18790.26630.30250.03640.01840.3336-0.05520.345321.546124.080530.2935
137.77476.05770.01828.2128-0.44624.8992-0.29430.79130.3263-0.45420.2405-0.2364-0.53360.3830.00480.30750.0299-0.01910.26630.0560.251912.127519.52818.9898
147.76511.49671.45314.59690.91035.6507-0.05780.16780.2085-0.16980.2207-0.4569-0.01890.649-0.15850.17510.00330.00390.1625-0.01310.216.637917.124913.66
154.1269-2.5075-1.99677.47841.97834.3989-0.111-0.15550.75690.1176-0.0457-0.1697-0.1501-0.26180.15650.201-0.0227-0.06030.1969-0.03490.26385.743618.85123.0951
168.8171-2.16162.77824.9596-2.24262.6666-0.16560.34590.1561-0.1690.0815-0.2403-0.02050.06190.09180.24230.0016-0.00060.2125-0.03610.166514.385114.758714.4597
178.4030.2284-5.07525.80572.99724.6485-0.02730.2680.2570.0364-0.10990.8642-0.0046-0.86760.16160.23190.0295-0.03520.2695-0.03960.3263-4.767815.505317.64
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 93 through 106 )B93 - 106
2X-RAY DIFFRACTION2chain 'B' and (resid 107 through 115 )B107 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid -7 through 5 )A-7 - 5
4X-RAY DIFFRACTION4chain 'A' and (resid 6 through 19 )A6 - 19
5X-RAY DIFFRACTION5chain 'A' and (resid 20 through 27 )A20 - 27
6X-RAY DIFFRACTION6chain 'A' and (resid 28 through 41 )A28 - 41
7X-RAY DIFFRACTION7chain 'A' and (resid 42 through 53 )A42 - 53
8X-RAY DIFFRACTION8chain 'A' and (resid 54 through 70 )A54 - 70
9X-RAY DIFFRACTION9chain 'A' and (resid 71 through 84 )A71 - 84
10X-RAY DIFFRACTION10chain 'A' and (resid 85 through 92 )A85 - 92
11X-RAY DIFFRACTION11chain 'A' and (resid 93 through 110 )A93 - 110
12X-RAY DIFFRACTION12chain 'B' and (resid -7 through 5 )B-7 - 5
13X-RAY DIFFRACTION13chain 'B' and (resid 6 through 27 )B6 - 27
14X-RAY DIFFRACTION14chain 'B' and (resid 28 through 47 )B28 - 47
15X-RAY DIFFRACTION15chain 'B' and (resid 48 through 74 )B48 - 74
16X-RAY DIFFRACTION16chain 'B' and (resid 75 through 84 )B75 - 84
17X-RAY DIFFRACTION17chain 'B' and (resid 85 through 92 )B85 - 92

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