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- PDB-4tzy: Vibrio vulnificus Adenine Riboswitch Variant, grown in both Sr2+ ... -

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Basic information

Entry
Database: PDB / ID: 4tzy
TitleVibrio vulnificus Adenine Riboswitch Variant, grown in both Sr2+ and Mg2+
ComponentsVibrio vulnificus Adenine Riboswitch
KeywordsRNA / riboswitch / gene regulation / adenine
Function / homologyADENINE / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsZhang, J. / Ferre-D'Amare, A.R.
CitationJournal: Structure / Year: 2014
Title: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Authors: Zhang, J. / Ferre-D'Amare, A.R.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Vibrio vulnificus Adenine Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,48411
Polymers22,6871
Non-polymers79710
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.283, 152.313, 24.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Vibrio vulnificus Adenine Riboswitch


Mass: 22687.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio vulnificus (bacteria)
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Mg, PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2014
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.57→41.4 Å / Num. obs: 6534 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 2 / Net I/σ(I): 15.3
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y26

1y26


Resolution: 2.57→41.375 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1171 10.09 %Random
Rwork0.2035 ---
obs0.2081 11606 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→41.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 19 21 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011688
X-RAY DIFFRACTIONf_angle_d0.3242623
X-RAY DIFFRACTIONf_dihedral_angle_d11.302849
X-RAY DIFFRACTIONf_chiral_restr0.017355
X-RAY DIFFRACTIONf_plane_restr0.00272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.68460.39651420.35061297X-RAY DIFFRACTION100
2.6846-2.82610.34341500.32071328X-RAY DIFFRACTION100
2.8261-3.00320.3361470.29241291X-RAY DIFFRACTION100
3.0032-3.2350.25811480.20761305X-RAY DIFFRACTION100
3.235-3.56030.2171450.18731326X-RAY DIFFRACTION100
3.5603-4.07510.24981370.18061291X-RAY DIFFRACTION100
4.0751-5.13270.19651520.15851295X-RAY DIFFRACTION100
5.1327-41.38060.23361500.17511302X-RAY DIFFRACTION100
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)
17.7833-1.7104-4.09894.77912.94215.91590.1465-0.84970.2873-0.364-0.50720.0362-0.75750.38160.25750.5837-0.1317-0.12960.64660.11931.5284-38.9522.005-11.675
25.87830.64020.121.3053-0.03053.48660.21941.1085-2.0001-0.3533-0.0861-0.50220.221-0.168-0.18340.44250.0045-0.03130.4256-0.1480.5149-28.25113.122-21.807
31.52320.64050.34022.38071.13590.59640.3871-0.395-0.12580.2029-0.1609-0.59750.1691-0.1882-0.20190.3506-0.0438-0.05830.39670.12330.3914-13.31230.398-6.07
42.04621.0364-0.24753.7655-0.29431.54310.149-0.2301-0.28970.1353-0.0811-0.7749-0.1090.0162-0.04250.34470.0601-0.00960.3172-0.01540.3863-15.60421.44-10.807
51.18021.342-0.41483.8871-1.04060.7503-0.2070.1196-1.3576-0.17470.23590.34850.31720.0304-0.01440.3993-0.0359-0.04680.60920.05740.7863-38.1415.954-15.542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN X AND RESID 13:18 )X13 - 18
2X-RAY DIFFRACTION2( CHAIN X AND RESID 19:23 )X19 - 23
3X-RAY DIFFRACTION3( CHAIN X AND RESID 24:43 )X24 - 43
4X-RAY DIFFRACTION4( CHAIN X AND RESID 44:72 )X44 - 72
5X-RAY DIFFRACTION5( CHAIN X AND RESID 73:83 )X73 - 83

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