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- PDB-10cx: Crystal structure of Pyrobaculum calidifontis Rpp30 -

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Basic information

Entry
Database: PDB / ID: 10cx
TitleCrystal structure of Pyrobaculum calidifontis Rpp30
ComponentsRpp30
KeywordsRNA BINDING PROTEIN / RNase P T type Archaeal
Function / homologyPolymerase/histidinol phosphatase-like / Uncharacterized protein
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 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: Rpp30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6943
Polymers19,8651
Non-polymers8292
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.228, 53.898, 42.213
Angle α, β, γ (deg.)90.000, 105.690, 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 Rpp30


Mass: 19864.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Gene: Pcal_0505 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A3MTG6
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The best diffracting crystals were grown by vapor diffusion equilibrated with 100 mM Tris-bicine, pH 8.5, 10% (w/v) PEG 20,000, 20% (v/v) PEG MME 550, 30 mM sodium nitrate, 30 mM disodium ...Details: The best diffracting crystals were grown by vapor diffusion equilibrated with 100 mM Tris-bicine, pH 8.5, 10% (w/v) PEG 20,000, 20% (v/v) PEG MME 550, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate. Crystals were sufficiently cryo-protected by the crystallization solution containing 20% (v/v) PEG MME 550 without further supplementation prior to flash freezing 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: 0.77484 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 10, 2013 / Details: Mirrors
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77484 Å / Relative weight: 1
ReflectionResolution: 0.897→40.64 Å / Num. obs: 97752 / % possible obs: 83.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 8.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.065 / Net I/σ(I): 13.8
Reflection shellResolution: 0.897→0.953 Å / Redundancy: 1.6 % / Rmerge(I) obs: 1.036 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4890 / CC1/2: 0.541 / Rrim(I) all: 1.151 / % possible all: 25.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.9→34.88 Å / SU ML: 0.0704 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1572 4987 5.1 %
Rwork0.1351 92761 -
obs0.1362 97748 83.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.21 Å2
Refinement stepCycle: LAST / Resolution: 0.9→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 56 208 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121862
X-RAY DIFFRACTIONf_angle_d1.23112565
X-RAY DIFFRACTIONf_chiral_restr0.0996291
X-RAY DIFFRACTIONf_plane_restr0.0118332
X-RAY DIFFRACTIONf_dihedral_angle_d13.7764771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.910.385940.186960X-RAY DIFFRACTION1.69
0.91-0.920.2925180.2642363X-RAY DIFFRACTION9.8
0.92-0.930.2517460.2453886X-RAY DIFFRACTION24.02
0.93-0.940.2998690.2431446X-RAY DIFFRACTION39.29
0.94-0.950.24931020.23931915X-RAY DIFFRACTION51.78
0.95-0.970.2681230.22712170X-RAY DIFFRACTION59.82
0.97-0.980.23841530.21582540X-RAY DIFFRACTION68.63
0.98-0.990.22441830.20562806X-RAY DIFFRACTION77.86
0.99-1.010.24911900.1943163X-RAY DIFFRACTION86.35
1.01-1.030.22451930.18043483X-RAY DIFFRACTION94.77
1.03-1.040.18391940.17213642X-RAY DIFFRACTION98.97
1.04-1.060.17811950.15333686X-RAY DIFFRACTION100
1.06-1.080.16321890.14173731X-RAY DIFFRACTION99.9
1.08-1.110.15531900.13143645X-RAY DIFFRACTION100
1.11-1.130.13141850.12293689X-RAY DIFFRACTION99.9
1.13-1.160.13991780.11843698X-RAY DIFFRACTION99.97
1.16-1.190.12482050.11633682X-RAY DIFFRACTION99.97
1.19-1.220.13942100.11263673X-RAY DIFFRACTION100
1.22-1.250.13222020.11343711X-RAY DIFFRACTION99.95
1.25-1.290.14582070.11283668X-RAY DIFFRACTION99.97
1.29-1.340.14021780.11373683X-RAY DIFFRACTION100
1.34-1.390.14041970.12043699X-RAY DIFFRACTION99.97
1.39-1.460.14781920.11653720X-RAY DIFFRACTION99.95
1.46-1.530.15121750.11543696X-RAY DIFFRACTION99.87
1.53-1.630.13082140.11443697X-RAY DIFFRACTION99.97
1.63-1.760.12892080.12363714X-RAY DIFFRACTION99.87
1.76-1.930.15631820.12913681X-RAY DIFFRACTION99.82
1.93-2.210.14521910.133702X-RAY DIFFRACTION99.92
2.21-2.790.15082010.14573742X-RAY DIFFRACTION99.97
2.79-34.880.17462130.14313770X-RAY DIFFRACTION99.8

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