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- PDB-4frn: Crystal structure of the cobalamin riboswitch regulatory element -

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Basic information

Entry
Database: PDB / ID: 4frn
TitleCrystal structure of the cobalamin riboswitch regulatory element
ComponentsCobalamin riboswitch aptamer domain
KeywordsRNA / cobalamin / riboswitch / B12
Function / homology: / Hydroxocobalamin / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesMarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.43 Å
AuthorsReyes, F.E. / Johnson, J.E. / Polaski, J.T. / Batey, R.T.
CitationJournal: Nature / Year: 2012
Title: B12 cofactors directly stabilize an mRNA regulatory switch.
Authors: Johnson, J.E. / Reyes, F.E. / Polaski, J.T. / Batey, R.T.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Cobalamin riboswitch aptamer domain
B: Cobalamin riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,16816
Polymers65,8292
Non-polymers4,33914
Water00
1
A: Cobalamin riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0848
Polymers32,9151
Non-polymers2,1697
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cobalamin riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0848
Polymers32,9151
Non-polymers2,1697
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.605, 81.833, 147.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain Cobalamin riboswitch aptamer domain


Mass: 32914.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was transcribed via in vitro T7 RNA polymerase / Source: (synth.) Marine metagenome (others)
#2: Chemical ChemComp-I2A / Hydroxocobalamin


Mass: 1345.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H88CoN13O15P
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba
Sequence detailsTHE SEQUENCE CAN BE FOUND AT GENBANK ACCESSION #: AACY021350931.1/557-477 OBTAINED FROM SHOTGUN ...THE SEQUENCE CAN BE FOUND AT GENBANK ACCESSION #: AACY021350931.1/557-477 OBTAINED FROM SHOTGUN SEQUENCING. THERE ARE SIX SUBSTITUTIONS TO THE ORIGINAL SEQUENCE TO FACILITATE CRYSTALLIZATION: UACUUG TO CGAAAG(THIS REGION OCCURS RESIDUE NUMBER 46 TO 51 IN THE PDB).

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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: 2.6 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 10% v/v MPD, 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetrahydrochloride, 80 mM potassium chloride, 20 mM barium chloride, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.6 Å
DetectorType: ADSC 315r / Detector: CCD / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 3.43→55.605 Å / Num. obs: 9466 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.082 / Net I/σ(I): 8.512
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.43-3.623.50.2982.6465613320.29899.5
3.62-3.843.40.2343.3443412870.23499.3
3.84-4.13.40.1844.2415812100.18499.6
4.1-4.433.50.1385.7396311310.138100
4.43-4.853.50.1027.6364410540.10299.7
4.85-5.433.40.0799.632859570.07999.7
5.43-6.273.40.06112.428998580.06199.7
6.27-7.673.30.04415.423697240.04499.2
7.67-10.853.30.0319.619045730.0398.9
10.85-55.630.0226.310123400.0296.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data processing
PDB_EXTRACT3.006data extraction
XDSdata reduction
SCALAdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FRG

4frg


Resolution: 3.43→54.83 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 450 4.77 %RANDOM
Rwork0.251 ---
all0.252 9428 --
obs0.252 9428 99.01 %-
Displacement parametersBiso max: 222.71 Å2 / Biso mean: 101.287 Å2 / Biso min: 52.57 Å2
Baniso -1Baniso -2Baniso -3
1--24.257 Å20 Å20 Å2
2---0.019 Å20 Å2
3---24.276 Å2
Refine analyzeLuzzati coordinate error obs: 0.854 Å
Refinement stepCycle: LAST / Resolution: 3.43→54.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4364 196 0 4560
LS refinement shellResolution: 3.43→3.83 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.305 133 5.12 %
Rwork0.248 2465 -
all0.251 2598 -
obs--99.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.48080.20961.19327.29772.76075.5264-0.06140.31620.0580.18730.1589-0.23020.08190.0227-0.09750.22990.0335-0.0334-0.29430.154-0.3063-12.012510.6524-32.4768
20.69280.22520.80563.73381.55187.65460.02340.03690.0242-0.01230.1403-0.22650.16140.0463-0.16370.15450.0595-0.0715-0.11820.1267-0.18614.305410.5036-66.8186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2B1 - 102

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