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- PDB-3pdr: Crystal structure of manganese bound M-box RNA -

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Basic information

Entry
Database: PDB / ID: 3pdr
TitleCrystal structure of manganese bound M-box RNA
ComponentsM-box Riboswitch RNA
KeywordsRNA / manganese-RNA complex
Function / homology: / : / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.853 Å
AuthorsRamesh, A. / Winkler, W.C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes.
Authors: Ramesh, A. / Wakeman, C.A. / Winkler, W.C.
History
DepositionOct 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: M-box Riboswitch RNA
A: M-box Riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,22933
Polymers103,6212
Non-polymers1,60831
Water9,872548
1
X: M-box Riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,58716
Polymers51,8111
Non-polymers77715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: M-box Riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,64217
Polymers51,8111
Non-polymers83116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-186 kcal/mol
Surface area44810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.780, 102.487, 126.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain M-box Riboswitch RNA


Mass: 51810.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: AL009126.3
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 10%MPD, 40mM sodium cacodylate, 12mM Spermine .4HCl,20mM KCl, 50mM Ammonium sulfate, 5mM MnCl2, pH 7.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.853→50 Å / Num. obs: 73903 / % possible obs: 96.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.853-1.895.60.91697.6
1.89-1.935.60.76898.1
1.93-1.965.60.6998
1.96-25.60.5497.8
2-2.055.70.48897.9
2.05-2.095.70.42197.7
2.09-2.155.70.34597.5
2.15-2.215.80.30797.5
2.21-2.275.80.27997.4
2.27-2.345.70.23697.2
2.34-2.435.80.19496.8
2.43-2.525.80.16897.1
2.52-2.645.80.13696.8
2.64-2.785.80.11696.9
2.78-2.955.80.09496.6
2.95-3.185.70.07696.9
3.18-3.55.70.06996.6
3.5-4.015.60.05596
4.01-5.055.60.04395.2
5.05-505.80.0491.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.49 Å
Translation2.5 Å47.49 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.853→47.488 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.27 / σ(F): 0.1 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 3497 5.05 %
Rwork0.1922 --
obs0.194 69314 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.72 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.023 Å2-0 Å20 Å2
2---2.2667 Å20 Å2
3---4.2897 Å2
Refinement stepCycle: LAST / Resolution: 1.853→47.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6862 31 548 7441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057674
X-RAY DIFFRACTIONf_angle_d1.42811956
X-RAY DIFFRACTIONf_dihedral_angle_d15.4653858
X-RAY DIFFRACTIONf_chiral_restr0.0661610
X-RAY DIFFRACTIONf_plane_restr0.007322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8531-1.87850.33971160.27542046X-RAY DIFFRACTION72
1.8785-1.90530.31811190.26082356X-RAY DIFFRACTION82
1.9053-1.93380.33551170.25912426X-RAY DIFFRACTION84
1.9338-1.9640.27241370.25462458X-RAY DIFFRACTION85
1.964-1.99620.29181400.24282466X-RAY DIFFRACTION87
1.9962-2.03060.30481340.22542526X-RAY DIFFRACTION87
2.0306-2.06750.29881340.22852581X-RAY DIFFRACTION90
2.0675-2.10730.28491510.21852566X-RAY DIFFRACTION90
2.1073-2.15030.26591460.20912621X-RAY DIFFRACTION90
2.1503-2.1970.23851410.2042591X-RAY DIFFRACTION91
2.197-2.24820.23051360.21222633X-RAY DIFFRACTION91
2.2482-2.30440.27131400.21712585X-RAY DIFFRACTION90
2.3044-2.36670.28221370.21972670X-RAY DIFFRACTION92
2.3667-2.43630.31671390.21952657X-RAY DIFFRACTION92
2.4363-2.5150.25081240.21852706X-RAY DIFFRACTION93
2.515-2.60480.26141460.22092693X-RAY DIFFRACTION93
2.6048-2.70910.25961530.22622732X-RAY DIFFRACTION94
2.7091-2.83240.26511570.23212729X-RAY DIFFRACTION95
2.8324-2.98170.25581420.20292788X-RAY DIFFRACTION96
2.9817-3.16850.2251410.18012808X-RAY DIFFRACTION95
3.1685-3.41310.17861480.16612823X-RAY DIFFRACTION96
3.4131-3.75640.20831440.15712827X-RAY DIFFRACTION96
3.7564-4.29970.1521560.13862827X-RAY DIFFRACTION95
4.2997-5.41590.161510.14072839X-RAY DIFFRACTION95
5.4159-47.50360.1871480.16762863X-RAY DIFFRACTION91

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