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- PDB-3dhs: Mapping metal-binding sites in the catalytic domain of bacterial ... -

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Basic information

Entry
Database: PDB / ID: 3dhs
TitleMapping metal-binding sites in the catalytic domain of bacterial RNase P RNA
ComponentsRNase P RNA
KeywordsHYDROLASE / RNA / CATALYTIC RNA / RNA PROCESSING
Function / homologyOSMIUM ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3.6 Å
AuthorsPace, N.R. / Kazantsev, A.V. / Krivenko, A.A.
CitationJournal: Rna / Year: 2009
Title: Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA
Authors: Kazantsev, A.V. / Krivenko, A.A. / Pace, N.R.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNase P RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,85716
Polymers87,0041
Non-polymers2,85315
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.350, 160.010, 133.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: RNA chain RNase P RNA


Mass: 87003.711 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription and is naturally found in Bacillus stearothermophilus.
References: ribonuclease P
#2: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Os

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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: 4.52 Å3/Da / Density % sol: 72.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M cacodylate, 0.1 M potassium chloride, 0.02 M magnesium chloride, 0.001 M spermine tetrachloride, 23% 1,6-hexanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2cacodylate12
3potassium chloride11
4potassium chloride12
5magnesium chloride11
6magnesium chloride12
7spermine tetrachloride11
81,6-hexanediol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1401 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1401 Å / Relative weight: 1
ReflectionRedundancy: 13.64 % / Av σ(I) over netI: 10.2 / Number: 252493 / Rmerge(I) obs: 0.102 / Χ2: 1 / D res high: 3.6 Å / D res low: 42.07 Å / Num. obs: 18374 / % possible obs: 98.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
7.7442.07960.0631.0813.1776
6.157.7499.60.0910.8713.84253
5.386.1599.40.1090.8313.57162
4.885.3899.10.1660.9213.48150
4.534.8899.20.2731.0113.67161
4.274.5399.20.4471.0513.71116
4.054.2798.80.6041.0113.8568
3.884.0598.80.6711.0313.870
3.733.8898.50.6911.0613.7449
3.63.7398.60.7141.1713.6689
ReflectionResolution: 3.6→42.07 Å / Num. obs: 18374 / % possible obs: 98.7 % / Redundancy: 13.64 % / Rmerge(I) obs: 0.102 / Χ2: 1 / Net I/σ(I): 10.2 / Scaling rejects: 1894
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 13.66 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.9 / Num. measured all: 24484 / Num. unique all: 1786 / Χ2: 1.17 / % possible all: 98.6

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRMethod translation: &STRIP%trans_method
Phasing dm shellResolution: 3.6→500.01 Å / Delta phi final: 0.154 / FOM : 0.165 / Reflection: 34294

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Processing

Software
NameVersionClassificationNB
d*TREK9.6Ldata scaling
CNSrefinement
CNSphasing
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2a64

2a64


Resolution: 3.6→42.07 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.69 / Data cutoff high absF: 2541105 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC, GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, Acta Cryst. D, 52, 57-64 (1996)
Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2357 6.9 %RANDOM
Rwork0.29 ---
obs-18347 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso max: 462.91 Å2 / Biso mean: 209.908 Å2 / Biso min: 17.98 Å2
Baniso -1Baniso -2Baniso -3
1--40.84 Å20 Å20 Å2
2--2.13 Å20 Å2
3---38.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.81 Å0.71 Å
Luzzati d res low-5 Å
Luzzati sigma a1.37 Å1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4613 15 0 4628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d14.1
X-RAY DIFFRACTIONc_improper_angle_d1.42
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.6-3.830.5284047.20.47752380.0265642523896.64
3.83-4.120.38963940.373518594.75
4.12-4.540.36174130.3215530496.62
4.54-5.190.32933940.2913538098.21
5.19-6.540.31253990.2653540998.99
6.54-500.010.25343530.2586542197.53
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2OS.param

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