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- PDB-3wz0: On archaeal homologs of the human RNase P proteins Pop5 and Rpp30... -

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Basic information

Entry
Database: PDB / ID: 3wz0
TitleOn archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis
Components
  • Ribonuclease P protein component 2
  • Ribonuclease P protein component 3
KeywordsHYDROLASE / TIM barrel-like structure / RRM-like structure / pre-tRNA cleavage
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, Pop5 subunit / Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P, protein component 3, archaeal / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / RNase P subunit p30 / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases ...Ribonuclease P, Pop5 subunit / Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P, protein component 3, archaeal / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / RNase P subunit p30 / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component 3 / Ribonuclease P protein component 2
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsSuematsu, K. / Ueda, T. / Nakashima, T. / Kakuta, Y. / Kimura, M.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2015
Title: On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis.
Authors: Suematsu, K. / Ueda, T. / Nakashima, T. / Kakuta, Y. / Kimura, M.
History
DepositionSep 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ribonuclease P protein component 3
F: Ribonuclease P protein component 3
C: Ribonuclease P protein component 2
A: Ribonuclease P protein component 2


Theoretical massNumber of molelcules
Total (without water)78,7624
Polymers78,7624
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-37 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.347, 77.530, 114.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12E
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLYCC16 - 11816 - 118
21ASNASNGLYGLYAD16 - 11816 - 118
12TYRTYRVALVALEA12 - 21712 - 217
22TYRTYRVALVALFB12 - 21712 - 217

NCS ensembles :
ID
1
2

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Components

#1: Protein Ribonuclease P protein component 3 / RNase P component 3 / Rpp30


Mass: 25306.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: rnp3, TK1450 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JH47, ribonuclease P
#2: Protein Ribonuclease P protein component 2 / RNase P component 2 / Pop5


Mass: 14074.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: rnp2, TK1767 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JJ62, ribonuclease P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 20% PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→64.16 Å / Num. all: 15606 / Num. obs: 15606 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.54 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.857 / SU B: 26.403 / SU ML: 0.496 / Cross valid method: THROUGHOUT / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31757 827 5.3 %RANDOM
Rwork0.2707 ---
obs0.27321 14767 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 0 34 5063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195201
X-RAY DIFFRACTIONr_bond_other_d0.0040.025174
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9697006
X-RAY DIFFRACTIONr_angle_other_deg0.863311877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3385631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60921.931233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8481558
X-RAY DIFFRACTIONr_chiral_restr0.0590.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215741
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021237
X-RAY DIFFRACTIONr_mcbond_it1.7395.8882506
X-RAY DIFFRACTIONr_mcbond_other1.7375.8872505
X-RAY DIFFRACTIONr_mcangle_it2.9668.8313134
X-RAY DIFFRACTIONr_mcangle_other2.9658.8323135
X-RAY DIFFRACTIONr_scbond_it1.6276.2172695
X-RAY DIFFRACTIONr_scbond_other1.6276.2182696
X-RAY DIFFRACTIONr_scangle_other2.8619.2073870
X-RAY DIFFRACTIONr_long_range_B_refined5.02546.4425910
X-RAY DIFFRACTIONr_long_range_B_other5.01846.4535908
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C63940.1
12A63940.1
21E134060.09
22F134060.09
LS refinement shellResolution: 2.794→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 64 -
Rwork0.481 928 -
obs--86.87 %

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