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- PDB-1v76: Crystal Structure of Archaeal Ribonuclease P Protein Ph1771p from... -

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Basic information

Entry
Database: PDB / ID: 1v76
TitleCrystal Structure of Archaeal Ribonuclease P Protein Ph1771p from Pyrococcus horikoshii OT3
ComponentsRNase P protein Ph1771p
KeywordsRNA BINDING PROTEIN / Archaeal RNase P protein
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease P/MRP, subunit p29 / Ribonuclease P protein subunit RNP1 / 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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNumata, T. / Kakuta, Y. / Kimura, M.
CitationJournal: Rna / Year: 2004
Title: Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29
Authors: Numata, T. / Ishimatsu, I. / Kakuta, Y. / Tanaka, I. / Kimura, M.
History
DepositionDec 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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: RNase P protein Ph1771p
B: RNase P protein Ph1771p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5844
Polymers22,3922
Non-polymers1922
Water2,594144
1
A: RNase P protein Ph1771p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2922
Polymers11,1961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNase P protein Ph1771p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2922
Polymers11,1961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.133, 56.271, 71.756
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNase P protein Ph1771p


Mass: 11196.147 Da / Num. of mol.: 2 / Fragment: core region / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1771 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O59425, ribonuclease P
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.07 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0M ammonium sulfate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97972, 0.90
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979721
20.91
ReflectionResolution: 2→50 Å / Num. all: 25204 / Num. obs: 25204 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSC(QUANTUM)data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→30.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 205516.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2296 9.3 %RANDOM
Rwork0.209 ---
obs0.209 24588 97.1 %-
all-24588 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1876 Å2 / ksol: 0.3714 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.08 Å20 Å2-0.09 Å2
2---2.59 Å20 Å2
3---7.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 10 144 1670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 351 9 %
Rwork0.214 3537 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SO4_XPLOR.PARAMSO4_XPLOR.TOP

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