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- PDB-3q1q: Structure of a Bacterial Ribonuclease P Holoenzyme in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 3q1q
TitleStructure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA
Components
  • RNase P RNA
  • Ribonuclease P protein component
  • TRNA (PHE)
KeywordsHYDROLASE/RNA / RNase P / ribozyme / ribonuclease P / tRNA / pre-tRNA / tetraloop-receptor / ribose zipper / a-minor interaction / base stacking / intermolecular base pairs / intermolecular RNA-RNA contacts / RNP / ribonucleoprotein complex / enzyme-product complex / metalloenzyme / RNA-metal interactions / shape complementarity / hydrolase-RNA complex / endonuclease
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P protein component
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å
AuthorsReiter, N.J. / Osterman, A. / Torres-Larios, A. / Swinger, K.K. / Pan, T. / Mondragon, A.
CitationJournal: Nature / Year: 2010
Title: Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA.
Authors: Reiter, N.J. / Osterman, A. / Torres-Larios, A. / Swinger, K.K. / Pan, T. / Mondragon, A.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionMar 9, 2011ID: 3OK7
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNase P RNA
A: Ribonuclease P protein component
C: TRNA (PHE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9319
Polymers154,6443
Non-polymers2876
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-92 kcal/mol
Surface area71330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.290, 169.290, 184.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNase P RNA


Mass: 112622.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
#2: Protein Ribonuclease P protein component / / RNase P protein / RNaseP protein / Protein C5


Mass: 14363.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rnpA, RNPA OR TM1463, RNPB, TM_1463 / Plasmid: PGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q9X1H4, ribonuclease P
#3: RNA chain TRNA (PHE)


Mass: 27658.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.95 Å3/Da / Density % sol: 75.14 %
Description: DUE TO THE ANISOTROPIC NATURE OF THE DIFFRACTION, THE DATA WERE TREATED IN TWO DIFFERENT WAYS: 1) BY APPLYING AN ANISOTROPIC CORRECTION TO THE DATA (ANISOTROPIC), AND 2) WITHOUT ANY ...Description: DUE TO THE ANISOTROPIC NATURE OF THE DIFFRACTION, THE DATA WERE TREATED IN TWO DIFFERENT WAYS: 1) BY APPLYING AN ANISOTROPIC CORRECTION TO THE DATA (ANISOTROPIC), AND 2) WITHOUT ANY ANISOTROPY CORRECTION (ISOTROPIC). WHILE COMPLETENESS OF THE HIGHEST RESOLUTION SHELL MAY APPEAR OF POOR QUALITY IN THE ANISOTROPIC CASE, THE DATA COLLECTION STATISTICS AND RWORK AND RFREE REFINEMENT STATISTICS WERE ACTUALLY BETTER FOR THE CARVED (ANISOTROPIC) DATA SET THAN FOR THE ISOTROPIC CASE. FOR THIS REASON, THE REPORTED 3Q1Q STRUCTURE AND HEADER REMARKS REFLECT THE CARVED, ANISOTROPICALLY CORRECTED DATA.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 1.8M Lithium sulfate, 0.05M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 20, 2009 / Details: MIRRORS
RadiationMonochromator: DIAMOND LAUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 27116 / % possible obs: 88.5 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 129.78 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.096 / Net I/σ(I): 12.2
Reflection shellResolution: 3.8→3.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.432 / % possible all: 22.3

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Processing

Software
NameVersionClassification
XDSdata scaling
TNTrefinement
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
TNTphasing
RefinementMethod to determine structure: MIRAS
Starting model: 2A2E, 2A64, 1NZ0, 1EHZ

2a2e

2a64

1nz0

1ehz


Resolution: 3.8→28.97 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1368 5.05 %RANDOM
Rwork0.25 ---
obs0.251 27090 --
Displacement parametersBiso mean: 80.04 Å2
Baniso -1Baniso -2Baniso -3
1--23.4702 Å20 Å20 Å2
2---23.4702 Å20 Å2
3---46.9404 Å2
Refine analyzeLuzzati coordinate error obs: 0.87 Å
Refinement stepCycle: LAST / Resolution: 3.8→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 9168 14 0 10155
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.007112442
X-RAY DIFFRACTIONt_angle_deg1.24173002
X-RAY DIFFRACTIONt_dihedral_angle_d55272
X-RAY DIFFRACTIONt_trig_c_planes202
X-RAY DIFFRACTIONt_gen_planes5665
X-RAY DIFFRACTIONt_it1124420
X-RAY DIFFRACTIONt_nbd15
LS refinement shellResolution: 3.8→3.94 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2334 27 4.62 %
Rwork0.2497 558 -
all0.2489 585 -

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