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- PDB-1ddy: MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER -

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Basic information

Entry
Database: PDB / ID: 1ddy
TitleMOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER
ComponentsVITAMIN B12 BINDING RNA
KeywordsRNA / TRIPLEX / VITAMIN B12 / APTAMER
Function / homologyCOBALAMIN / METHYLAMINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 3 Å
AuthorsSussman, D. / Nix, J.C. / Wilson, C.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The structural basis for molecular recognition by the vitamin B 12 RNA aptamer.
Authors: Sussman, D. / Nix, J.C. / Wilson, C.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Oct 24, 2012Group: Non-polymer description
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: VITAMIN B12 BINDING RNA
C: VITAMIN B12 BINDING RNA
E: VITAMIN B12 BINDING RNA
G: VITAMIN B12 BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,56912
Polymers45,1234
Non-polymers5,4468
Water00
1
A: VITAMIN B12 BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6423
Polymers11,2811
Non-polymers1,3612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: VITAMIN B12 BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6423
Polymers11,2811
Non-polymers1,3612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: VITAMIN B12 BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6423
Polymers11,2811
Non-polymers1,3612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: VITAMIN B12 BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6423
Polymers11,2811
Non-polymers1,3612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.330, 161.880, 100.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: RNA chain
VITAMIN B12 BINDING RNA


Mass: 11280.819 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: SEQUENCE RESULTS FROM IN VITRO SELECTION EXPERIMENTS
#2: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical
ChemComp-NME / METHYLAMINE


Mass: 31.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N

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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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: LICL, ISOPROPANOL, MGCL2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1LICL11
2MGCL211
3ISOPROPANOL11
4ISOPROPANOL12
Crystal grow
*PLUS
pH: 6.5 / Details: Sussman, D., (1999) Acta Cryst., D55, 326.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 %2-propanol1reservoir
215 mM1reservoirMgCl2
320 mMK-PIPES1reservoir
40.5 mM1reservoirBaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.6047,1.6057,1.5842
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.60471
21.60571
31.58421
ReflectionResolution: 3→20 Å / Num. all: 40156 / Num. obs: 40156 / % possible obs: 92 % / Redundancy: 3.85 % / Rsym value: 0.061 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.469 / Rsym value: 0.195 / % possible all: 80
Reflection
*PLUS
Highest resolution: 3 Å

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD PHASING / Resolution: 3→12 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 3943390.88 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: FOR CONSISTENCY, SUGARS PUCKERS WERE RESTRAINED TO THE A-RNA C3'-ENDO CONFORMATION. THIS MIGHT CONTRIBUTE TO THE HIGH RMSD FROM IDEAL VALUES OF IMPROPER ANGLES
RfactorNum. reflection% reflectionSelection details
Rfree0.246 663 5 %RANDOM
Rwork0.204 ---
obs0.204 13252 87.9 %-
all-16492 --
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-15.23 Å20 Å20 Å2
2---21.17 Å20 Å2
3---5.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3004 372 0 3376
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 119 5.9 %
Rwork0.283 1886 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP_JHC.PARAM&_1_TOP_1
X-RAY DIFFRACTION2B12.PARAM&_1_TOP_2
X-RAY DIFFRACTION3ION.PARAM&_1_TOP_3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.283

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