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- PDB-1nbs: Crystal structure of the specificity domain of Ribonuclease P RNA -

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Basic information

Entry
Database: PDB / ID: 1nbs
TitleCrystal structure of the specificity domain of Ribonuclease P RNA
ComponentsRIBONUCLEASE P RNA
KeywordsRNA / Ribonuclease P RNA / P RNA / S-domain
Function / homologyLEAD (II) ION / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å
AuthorsKrasilnikov, A.S. / Yang, X. / Pan, T. / Mondragon, A.
CitationJournal: Nature / Year: 2003
Title: Crystal structure of the specificity domain of Ribonuclease P
Authors: Krasilnikov, A.S. / Yang, X. / Pan, T. / Mondragon, A.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Base A240 is a transcriptional artifact.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE P RNA
B: RIBONUCLEASE P RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,47737
Polymers100,4202
Non-polymers5,05735
Water00
1
A: RIBONUCLEASE P RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,81818
Polymers50,2101
Non-polymers2,60817
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE P RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,65919
Polymers50,2101
Non-polymers2,44918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.5, 145.3, 144.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain RIBONUCLEASE P RNA


Mass: 50209.945 Da / Num. of mol.: 2 / Fragment: Specificity-domain, S-domain / Mutation: U86G, A239C, U89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Description: The RNA was produced by vitro transcription with T7 polymerase from a pUC19-based template which contained cloned sequence of the S-domain.
Plasmid: pUC19 / Production host: Bacillus subtilis (bacteria) / References: GenBank: 143351
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Pb

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: isopropanol, strontium chloride, magnesium chloride, spermine, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlRNA1drop
210.5 %(v/v)isopropanol1reservoir
380 mM1reservoirSrCl2
45 mM1reservoirMgCl2
51.5 mMspermine1reservoir
650 mMMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9475,0.9293
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2002 / Details: mirrors
RadiationMonochromator: Si MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94751
20.92931
ReflectionResolution: 3.15→33 Å / Num. all: 23276 / Num. obs: 23276 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 66.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.8
Reflection shellResolution: 3.15→3.24 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1345 / Rsym value: 0.272 / % possible all: 80.9
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 231005 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 80.9 % / Rmerge(I) obs: 0.272

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
SHARPphasing
CNSrefinement
XDSdata scaling
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.15→33 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.847 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.515
Details: Bases 143-165, 201-212 in molecule A and 121-124 and 240 in molecule B are disordered; only phosphate backbone could be traced for bases 99 and 101 in both molecules. CNS was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.30736 1173 5.1 %RANDOM
Rwork0.28043 ---
all0.28179 22853 --
obs0.28179 21680 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.249 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å20 Å20 Å2
2---0.56 Å20 Å2
3----3.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.515 Å0.5687 Å
Refinement stepCycle: LAST / Resolution: 3.15→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5802 35 0 5837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216497
X-RAY DIFFRACTIONr_angle_refined_deg1.291310124
X-RAY DIFFRACTIONr_chiral_restr0.1390.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022832
X-RAY DIFFRACTIONr_nbd_refined0.2810.33164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.393
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.58
X-RAY DIFFRACTIONr_scbond_it1.48736497
X-RAY DIFFRACTIONr_scangle_it2.4174.510124
LS refinement shellResolution: 3.154→3.235 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 66
Rwork0.354 1260
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 33 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.29
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it

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