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- PDB-10cw: Crystal structure of Thermoproteus neutrophilus Rpp30 -

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Basic information

Entry
Database: PDB / ID: 10cw
TitleCrystal structure of Thermoproteus neutrophilus Rpp30
ComponentsRibonuclease P Rpp30
KeywordsRNA BINDING PROTEIN / RNase P T type Archaeal
Function / homologyPolymerase/histidinol phosphatase-like / Uncharacterized protein
Function and homology information
Biological speciesPyrobaculum neutrophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 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

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Assembly

Deposited unit
A: Ribonuclease P Rpp30
B: Ribonuclease P Rpp30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,88916
Polymers40,0202
Non-polymers86914
Water5,441302
1
A: Ribonuclease P Rpp30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,56910
Polymers20,0101
Non-polymers5599
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease P Rpp30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3206
Polymers20,0101
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.758, 66.368, 66.056
Angle α, β, γ (deg.)90.000, 113.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ribonuclease P Rpp30


Mass: 20009.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein expressed with an N-terminal His6 affinity tag that is removable by TEV protease leaving three amino acids at the N-terminus (SNA)
Source: (gene. exp.) Pyrobaculum neutrophilum (archaea) / Gene: Rpp30 / Plasmid: pMSCG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B1YD41
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Crystals were grown by vapor diffusion equilibrated with 100 mM CHES, pH 9.5, 35% (v/v) PEG 400 at 303 K. Crystals were sufficiently cryo-protected by the crystallization solution containing ...Details: Crystals were grown by vapor diffusion equilibrated with 100 mM CHES, pH 9.5, 35% (v/v) PEG 400 at 303 K. Crystals were sufficiently cryo-protected by the crystallization solution containing 35% (v/v) PEG 400 without further supplementation prior to flash freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9211 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 6, 2013 / Details: Mirrors
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9211 Å / Relative weight: 1
ReflectionResolution: 1.4→44.7 Å / Num. obs: 60247 / % possible obs: 74.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 12.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.217 / Rrim(I) all: 0.227 / Net I/σ(I): 11
Reflection shellResolution: 1.43→1.6 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.218 / Num. unique obs: 3012 / CC1/2: 0.974 / Rrim(I) all: 0.234 / % possible all: 16.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.20.1_4487refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.43→32.97 Å / SU ML: 0.1364 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 26.8686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 3038 5.04 %Random selection
Rwork0.1943 57184 --
obs0.1963 60222 74.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.43→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 56 302 3122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01253031
X-RAY DIFFRACTIONf_angle_d1.21884144
X-RAY DIFFRACTIONf_chiral_restr0.0977481
X-RAY DIFFRACTIONf_plane_restr0.0151537
X-RAY DIFFRACTIONf_dihedral_angle_d16.25061191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.381640.321644X-RAY DIFFRACTION1.32
1.46-1.480.2523110.2481137X-RAY DIFFRACTION4.14
1.48-1.50.3387290.1971423X-RAY DIFFRACTION12.24
1.5-1.530.2615430.1828837X-RAY DIFFRACTION24.24
1.53-1.560.2353820.16791328X-RAY DIFFRACTION38.52
1.56-1.590.19641050.15721890X-RAY DIFFRACTION54.39
1.59-1.630.24731120.14452274X-RAY DIFFRACTION64.75
1.63-1.670.19631190.14542521X-RAY DIFFRACTION72.41
1.67-1.710.19371440.14452792X-RAY DIFFRACTION80.28
1.71-1.750.18741450.15533043X-RAY DIFFRACTION86.91
1.75-1.80.17912180.15863341X-RAY DIFFRACTION96.66
1.8-1.860.18281740.1653481X-RAY DIFFRACTION100
1.86-1.930.21261890.17453509X-RAY DIFFRACTION100
1.93-2.010.23382040.20263466X-RAY DIFFRACTION99.97
2.01-2.10.2821760.23713472X-RAY DIFFRACTION99.95
2.1-2.210.26761590.22753535X-RAY DIFFRACTION99.89
2.21-2.350.28641840.23123482X-RAY DIFFRACTION99.95
2.35-2.530.26081770.22933521X-RAY DIFFRACTION99.97
2.53-2.780.26952160.24433463X-RAY DIFFRACTION100
2.78-3.190.24881770.22543534X-RAY DIFFRACTION100
3.19-4.010.2321930.17523518X-RAY DIFFRACTION100
4.01-32.970.19281770.17043573X-RAY DIFFRACTION99

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