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- PDB-1ts9: Crystal Structure of the Archaeal Homolog of Human RNase P Protei... -

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Basic information

Entry
Database: PDB / ID: 1ts9
TitleCrystal Structure of the Archaeal Homolog of Human RNase P Protein Rpp29 from Archaeoglobus fulgidus
ComponentsRibonuclease P protein component 1
KeywordsHYDROLASE / anti-parallel / beta-sheet / alpha helix / internal salt bridge / selenomethionine / 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 / SAD / 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)12,1111
Polymers12,1111
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.905, 71.769, 32.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 12110.521 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.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 32.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, Ammonium Sulfate, pH 7.5, 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: Feb 9, 2004 / 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: 17764 / Num. obs: 17599 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.67→1.72 Å / % possible all: 90.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2391 1670 random
Rwork0.2037 --
all0.211 17764 -
obs0.213 17599 -
Displacement parametersBiso mean: 22.2531 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 0 122 911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_angle_deg1.3509
X-RAY DIFFRACTIONc_dihedral_angle_d23.193
X-RAY DIFFRACTIONc_improper_angle_d0.62551
X-RAY DIFFRACTIONc_mcbond_it1.279
X-RAY DIFFRACTIONc_mcangle_it1.89
X-RAY DIFFRACTIONc_scbond_it2.413
X-RAY DIFFRACTIONc_scangle_it3.414
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.2751 154 -
Rwork0.2349 --
obs-1533 92 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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