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- PDB-2av5: Crystal structure of Pyrococcus furiosus Pop5, an archaeal Ribonu... -

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Basic information

Entry
Database: PDB / ID: 2av5
TitleCrystal structure of Pyrococcus furiosus Pop5, an archaeal Ribonuclease P protein
ComponentsRibonuclease P protein component 2
KeywordsHYDROLASE / RIBONUCLEASE P
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / cytoplasm
Similarity search - Function
Ribonuclease P, Pop5 subunit / Ribonuclease P protein subunit Rnp2, archaea / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component 2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SIR / Resolution: 3.15 Å
AuthorsWilson, R.C. / Bohlen, C.J. / Foster, M.P. / Bell, C.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of Pfu Pop5, an archaeal RNase P protein.
Authors: Wilson, R.C. / Bohlen, C.J. / Foster, M.P. / Bell, C.E.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Feb 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 protein component 2
B: Ribonuclease P protein component 2
C: Ribonuclease P protein component 2
D: Ribonuclease P protein component 2
E: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)69,2365
Polymers69,2365
Non-polymers00
Water00
1
A: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)13,8471
Polymers13,8471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)13,8471
Polymers13,8471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)13,8471
Polymers13,8471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)13,8471
Polymers13,8471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)13,8471
Polymers13,8471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.500, 107.500, 179.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Ribonuclease P protein component 2 / RNase P component 2


Mass: 13847.177 Da / Num. of mol.: 5 / Mutation: C72S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rnp2 / Plasmid: PET-33B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U151, ribonuclease P

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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: 3.72 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: Imidazole, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 8, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.15→46.9 Å / Num. obs: 17989 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.15→3.35 Å / % possible all: 70

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
MLPHAREphasing
RefinementMethod to determine structure: SIR / Resolution: 3.15→46.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 315763.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1773 9.9 %RANDOM
Rwork0.232 ---
obs0.232 17989 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.2697 Å2 / ksol: 0.259097 e/Å3
Displacement parametersBiso mean: 88.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 3.15→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 0 0 4315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 293 10 %
Rwork0.37 2648 -
obs--96.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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