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- PDB-10da: Crystal structure of Pyrobaculum islandicum L7Ae -

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Basic information

Entry
Database: PDB / ID: 10da
TitleCrystal structure of Pyrobaculum islandicum L7Ae
ComponentsLarge ribosomal subunit protein eL8
KeywordsRNA BINDING PROTEIN / RNase P T type Archaeal
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesPyrobaculum islandicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.998 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: Large ribosomal subunit protein eL8
B: Large ribosomal subunit protein eL8
C: Large ribosomal subunit protein eL8
D: Large ribosomal subunit protein eL8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25210
Polymers65,8214
Non-polymers4316
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.852, 60.000, 60.710
Angle α, β, γ (deg.)87.134, 75.531, 84.241
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Large ribosomal subunit protein eL8


Mass: 16455.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum islandicum (archaea) / Gene: rpl7ae, Pisl_0589 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta (DE3) / Variant (production host): Rosetta / References: UniProt: A1RS35
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were grown by vapor diffusion in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 at 303 K. Crystals were cryo- ...Details: Crystals were grown by vapor diffusion in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 at 303 K. Crystals were cryo-protected in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 22.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 and 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-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2016 / Details: Mirrors
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 0.998→19.89 Å / Num. obs: 203846 / % possible obs: 70.9 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.027 / Net I/σ(I): 14.3
Reflection shellResolution: 0.998→1.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 37675 / CC1/2: 0.602 / Rrim(I) all: 0.548 / % possible all: 17.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.998→19.89 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.928 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.151 9969 4.891 %
Rwork0.1363 193870 -
all0.137 --
obs-203839 70.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.665 Å20.714 Å20.105 Å2
2---0.625 Å2-0.666 Å2
3---1.323 Å2
Refinement stepCycle: LAST / Resolution: 0.998→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 0 20 445 4808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125084
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165209
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.887027
X-RAY DIFFRACTIONr_angle_other_deg0.4971.7812201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.093530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23410948
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.71710206
X-RAY DIFFRACTIONr_chiral_restr0.0780.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025997
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02967
X-RAY DIFFRACTIONr_nbd_refined0.2240.2957
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24250
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22370
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1480.24
X-RAY DIFFRACTIONr_metal_ion_refined0.050.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.235
X-RAY DIFFRACTIONr_nbd_other0.1720.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0770.22
X-RAY DIFFRACTIONr_mcbond_it2.5411.0172531
X-RAY DIFFRACTIONr_mcbond_other2.5311.0172531
X-RAY DIFFRACTIONr_mcangle_it4.1621.8373215
X-RAY DIFFRACTIONr_mcangle_other4.1631.8383216
X-RAY DIFFRACTIONr_scbond_it3.4351.2372553
X-RAY DIFFRACTIONr_scbond_other3.4341.2372554
X-RAY DIFFRACTIONr_scangle_it5.2962.1693743
X-RAY DIFFRACTIONr_scangle_other5.2962.1693744
X-RAY DIFFRACTIONr_lrange_it11.08215.815570
X-RAY DIFFRACTIONr_lrange_other11.08115.8115571
X-RAY DIFFRACTIONr_rigid_bond_restr2.542310293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.998-1.0240.403790.4941435X-RAY DIFFRACTION7.1452
1.024-1.0520.3911870.3893593X-RAY DIFFRACTION18.29
1.052-1.0820.3193420.2946514X-RAY DIFFRACTION34.0586
1.082-1.1150.2574900.259113X-RAY DIFFRACTION49.4694
1.115-1.1520.1985800.20211015X-RAY DIFFRACTION61.126
1.152-1.1920.1936120.17312334X-RAY DIFFRACTION70.8283
1.192-1.2370.1756790.15913881X-RAY DIFFRACTION82.4089
1.237-1.2870.1697670.14614667X-RAY DIFFRACTION90.7562
1.287-1.3440.1447230.12914368X-RAY DIFFRACTION92.6112
1.344-1.410.1457280.11713811X-RAY DIFFRACTION93.3004
1.41-1.4850.1336720.1113256X-RAY DIFFRACTION93.9557
1.485-1.5750.1186620.10112570X-RAY DIFFRACTION94.548
1.575-1.6830.126710.10111924X-RAY DIFFRACTION95.2507
1.683-1.8170.1335550.10411186X-RAY DIFFRACTION95.8449
1.817-1.9890.1325450.11110350X-RAY DIFFRACTION96.4671
1.989-2.220.1424120.129520X-RAY DIFFRACTION97.049
2.22-2.5590.1384320.1258399X-RAY DIFFRACTION97.6881
2.559-3.1210.1483760.1457128X-RAY DIFFRACTION98.2327
3.121-4.360.1472910.1435608X-RAY DIFFRACTION98.7776
4.36-19.890.1911660.1863197X-RAY DIFFRACTION98.8536

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