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- PDB-10cy: Crystal structure of Pyrobaculum islandicum Rpp30/Pop5 complex -

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Basic information

Entry
Database: PDB / ID: 10cy
TitleCrystal structure of Pyrobaculum islandicum Rpp30/Pop5 complex
Components
  • Pop5
  • Rpp30
KeywordsRNA BINDING PROTEIN / RNase P T type Archaeal
Function / homologyPolymerase/histidinol phosphatase-like / : / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesPyrobaculum islandicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChan, C.W. / Mondragon, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118108 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM058443 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)4T32 GM008152 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32 GM008382 United States
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Crystal structures of type T archaeal ribonuclease P Rpp30, Rpp30/Pop5, and L7Ae provide insights into a reduced RNase P.
Authors: Chan, C.W. / Mondragon, A.
History
DepositionJan 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rpp30
B: Rpp30
C: Pop5
D: Pop5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2306
Polymers61,1524
Non-polymers782
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.217, 108.217, 139.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "C" and resid 2 through 90)
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ARGARGAA6 - 1746 - 174
d_2ens_1ARGARGBB6 - 1746 - 174
d_1ens_2VALVALCC2 - 902 - 90
d_2ens_2VALVALDD2 - 902 - 90

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.949298091386, 0.0660884125639, 0.307352331072), (0.0343205108491, -0.950024701226, 0.310282402975), (0.312498377957, 0.305098981948, 0.899588447563)149.451173407, 35.4672311145, -30.0257205939
2given(-0.954032855819, 0.0492182942252, 0.295632998041), (0.0423415406075, -0.954394206619, 0.295531541989), (0.296695979002, 0.29446435758, 0.908439452115)150.513964979, 35.4261749138, -29.0684133551

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Components

#1: Protein Rpp30


Mass: 19912.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum islandicum (archaea) / Gene: Pisl_1749 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A1RVB8
#2: Protein Pop5


Mass: 10663.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum islandicum (archaea) / Gene: Pisl_1748 / Plasmid: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3) / References: UniProt: A1RVB7
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were grown from 1-2 mg/ml protein stock solutions at 303 K by vapor diffusion over a narrow range of equilibration solutions optimized around 100 mM Tris-HCl, pH 8.5, 200 mM KCl, ...Details: Crystals were grown from 1-2 mg/ml protein stock solutions at 303 K by vapor diffusion over a narrow range of equilibration solutions optimized around 100 mM Tris-HCl, pH 8.5, 200 mM KCl, 20% (v/v) ethanol. Crystals were cryo-protected by supplementing the crystallization solutions with 25% glycerol (v/v) and subsequently flash frozen with liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1051 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2016 / Details: Mirrors
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionResolution: 2.49→48.4 Å / Num. obs: 27135 / % possible obs: 91.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 50.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Net I/σ(I): 11.7
Reflection shellResolution: 2.49→2.6 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8812 / CC1/2: 0.632 / Rrim(I) all: 1.44 / % possible all: 37.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.4 Å / SU ML: 0.3194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 1354 4.99 %
Rwork0.1992 25774 -
obs0.2015 27128 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.58 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 2 44 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564185
X-RAY DIFFRACTIONf_angle_d0.83535689
X-RAY DIFFRACTIONf_chiral_restr0.0504689
X-RAY DIFFRACTIONf_plane_restr0.0085703
X-RAY DIFFRACTIONf_dihedral_angle_d18.24821573
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.501128506146
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.717399285309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.570.3084510.2639805X-RAY DIFFRACTION29.33
2.58-2.680.32721170.28832346X-RAY DIFFRACTION84.55
2.68-2.80.33581530.29052742X-RAY DIFFRACTION99.11
2.8-2.950.3521300.24362797X-RAY DIFFRACTION100
2.95-3.130.27491510.2192780X-RAY DIFFRACTION99.9
3.13-3.370.2811550.22182787X-RAY DIFFRACTION100
3.37-3.710.24641480.19092819X-RAY DIFFRACTION99.83
3.71-4.250.21611440.17462833X-RAY DIFFRACTION99.67
4.25-5.350.17451530.16152860X-RAY DIFFRACTION99.18
5.35-48.40.24931520.19573005X-RAY DIFFRACTION99.06

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