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- PDB-1tsf: Crystal Structure of the Archaeal homolog of Human RNase P Protei... -

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Basic information

Entry
Database: PDB / ID: 1tsf
TitleCrystal Structure of the Archaeal homolog of Human RNase P Protein Rpp29 from Archaeoglobus fulgidus
ComponentsRibonuclease P protein component 1
KeywordsHYDROLASE / Beta sheet / alpha helix / anti-parallel / internal salt-bridge / SM-fold
Function / homology
Function and homology information


ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / rRNA processing / cytoplasm
Similarity search - Function
Ribonuclease P/MRP, subunit p29 / Ribonuclease P protein subunit RNP1 / Ribonuclease P/MRP subunit Rpp29 / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Ribonuclease P protein component 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSidote, D.J. / Heideker, J. / Hoffman, D.W.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus.
Authors: Sidote, D.J. / Heideker, J. / Hoffman, D.W.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
A: Ribonuclease P protein component 1


Theoretical massNumber of molelcules
Total (without water)11,8291
Polymers11,8291
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.565, 43.790, 49.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease P protein component 1 / RNase P component 1 / aRpp29


Mass: 11829.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: RNP1, AF1917 / Plasmid: pMAL-c2t / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O28362, ribonuclease P
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate, Ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. all: 9848 / Num. obs: 8583 / % possible obs: 87.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 %
Reflection shellResolution: 1.7→1.76 Å / % possible all: 98.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TS9

1ts9


Resolution: 1.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.283 902 random
Rwork0.25 --
obs0.25 8583 -
all-9848 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.126 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.554 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms649 0 0 99 748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.36
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.57
LS refinement shellResolution: 1.7→1.73 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.519 47 -
Rwork0.473 --
obs-411 78.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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