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- PDB-2a64: Crystal Structure of Bacterial Ribonuclease P RNA -

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Basic information

Entry
Database: PDB / ID: 2a64
TitleCrystal Structure of Bacterial Ribonuclease P RNA
Componentsribonuclease P RNA
KeywordsHYDROLASE / RNA / ribonuclease / ribozyme
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsKazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structure of a bacterial ribonuclease P RNA.
Authors: Kazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonuclease P RNA


Theoretical massNumber of molelcules
Total (without water)135,3041
Polymers135,3041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.150, 159.420, 410.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: RNA chain ribonuclease P RNA


Mass: 135304.172 Da / Num. of mol.: 1 / Mutation: G417C / Source method: obtained synthetically
Details: This sequence is naturally present in Bacillus stearothermophilus (strain 1430R) as gene product of rnpB. The gene was cloned in plasmid pBstHH2, with a mutation G417C. Large quantities were ...Details: This sequence is naturally present in Bacillus stearothermophilus (strain 1430R) as gene product of rnpB. The gene was cloned in plasmid pBstHH2, with a mutation G417C. Large quantities were produces as run-off transcription in vitro with phage T7 RNA polymerase
References: GenBank: 143442

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.270.7
24.270.7
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: (NH4)2SO4, K2SO4, MgCl2, MPD, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2K2SO411
3MgCl211
4MPD11
5(NH4)2SO412
6K2SO412
7MgCl212
8MPD12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONSSRL BL9-221.1397, 1.1402, 0.9540
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJul 1, 2003
ADSC QUANTUM 3152CCDJul 4, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.13971
31.14021
40.9541
ReflectionResolution: 3.3→500 Å / Num. obs: 35599 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.84 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 7.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.7data extraction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.3→37.15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 28550.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Used maximum likeliehood target using amplitudes and phase probability distribution throughout refinement. R(work), R(free) calculated for this target. R(all), R(observed) calculated for ...Details: Used maximum likeliehood target using amplitudes and phase probability distribution throughout refinement. R(work), R(free) calculated for this target. R(all), R(observed) calculated for standard crystallographic residual target.
RfactorNum. reflection% reflectionSelection details
Rfree0.3399 1798 5.1 %RANDOM
Rwork0.3204 ---
all0.3247 37397 --
obs0.3214 35599 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 154.4 Å2
Baniso -1Baniso -2Baniso -3
1-20.93 Å20 Å20 Å2
2---10.85 Å20 Å2
3----10.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.72 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.3→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6383 0 0 6383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d14.6
X-RAY DIFFRACTIONc_improper_angle_d1.39
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.442 191 5.5 %
Rwork0.421 3285 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna.topdna-rna_rep.param
X-RAY DIFFRACTION2NULLNULL

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