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- PDB-4xnr: Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized ... -

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Basic information

Entry
Database: PDB / ID: 4xnr
TitleVibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine
ComponentsVibrio Vulnificus Adenine Riboswitch
KeywordsRNA / Riboswitch
Function / homologyADENINE / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsZhang, J. / Liu, Y. / Wang, Y.-X. / Ferre-D'Amare, A.R.
CitationJournal: Nature / Year: 2015
Title: Synthesis and applications of RNAs with position-selective labelling and mosaic composition.
Authors: Liu, Y. / Holmstrom, E. / Zhang, J. / Yu, P. / Wang, J. / Dyba, M.A. / Chen, D. / Ying, J. / Lockett, S. / Nesbitt, D.J. / Ferre-D'Amare, A.R. / Sousa, R. / Stagno, J.R. / Wang, Y.X.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Vibrio Vulnificus Adenine Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9688
Polymers22,6871
Non-polymers2817
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.482, 154.682, 25.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.08 %
Description: Rectangular crystals with maximal dimensions of 250 x 50 x 50 micrometers
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: Apr 30, 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: 2.21→49.5 Å / Num. obs: 10358 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.658507554 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.92
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.67 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: dev_1839)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZX

4tzx


Resolution: 2.21→47.13 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.32 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.22 985 9.95 %Random selection
Rwork0.2 16846 --
obs0.21 10358 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.76 Å2
Refinement stepCycle: LAST / Resolution: 2.21→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 16 64 1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0009144356208311688
X-RAY DIFFRACTIONf_angle_d0.2743602048162623
X-RAY DIFFRACTIONf_chiral_restr0.0145149350427355
X-RAY DIFFRACTIONf_plane_restr0.0014222504387972
X-RAY DIFFRACTIONf_dihedral_angle_d11.0843343738849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.26660.3821440.3681291X-RAY DIFFRACTION98.49
2.2666-2.33320.3321440.3621281X-RAY DIFFRACTION99.92
2.3332-2.40860.3441430.3391284X-RAY DIFFRACTION100
2.4086-2.49460.4071510.3261348X-RAY DIFFRACTION99.93
2.4946-2.59450.3921380.3251253X-RAY DIFFRACTION99.5
2.5945-2.71260.3681360.3371304X-RAY DIFFRACTION99.86
2.7126-2.85560.3341420.31313X-RAY DIFFRACTION99.86
2.8556-3.03440.3061400.2771293X-RAY DIFFRACTION99.79
3.0344-3.26870.2141390.1941310X-RAY DIFFRACTION99.25
3.2687-3.59750.1771460.1761300X-RAY DIFFRACTION99.52
3.5975-4.11780.2081450.1711302X-RAY DIFFRACTION99.93
4.1178-5.1870.1831450.141276X-RAY DIFFRACTION99.93
5.187-47.130.1351490.1511291X-RAY DIFFRACTION99.11
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)
14.36160.8122-3.50145.12934.29187.72050.23020.1815-0.29490.30330.8601-0.6012-1.25590.3813-1.14930.52540.14080.01150.564-0.00560.40095.986517.84513.8268
22.2512-1.7743-2.67092.43561.79753.4037-0.01170.672-1.6436-0.169-0.79150.54810.0354-0.24740.78130.77730.2398-0.02230.87940.00311.399712.54623.41111.5239
33.0088-1.16520.84814.4695-1.59151.88420.29590.2432-0.067-0.4089-0.23690.6740.1418-0.0285-0.04560.42490.0753-0.04720.4805-0.10150.4838-10.790727.6976-3.7608
42.2483-0.7038-0.36313.3374-1.27140.63780.18160.27440.1511-0.0028-0.39880.033-0.22670.31130.11010.48780.0723-0.0520.5723-0.1570.4751-1.751232.2687-1.3236
55.79212.07421.97595.4702-0.19574.346-0.37560.155-0.1294-0.32850.17630.3592-0.55850.31960.18620.48220.1320.03660.4278-0.04580.3555-0.569219.5853-1.3402
64.97560.17640.28741.88711.5313.50820.69550.7668-1.4764-0.3632-0.90032.3528-0.0759-0.79740.35720.63180.145-0.18710.7778-0.09231.6608-28.370825.356-7.1179
71.7882-1.41750.29443.9279-0.5692.10150.0312-0.1116-0.23370.3634-0.05980.9282-0.1882-0.0712-0.03690.5604-0.0011-0.08770.477-0.04390.7436-14.393719.8704-2.1986
80.9842-0.32450.73644.43931.01452.5102-0.24380.2574-1.65550.21510.5055-0.57920.1144-0.2037-0.35110.52770.12530.01060.6963-0.06191.011513.99755.5562.8704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN X AND RESID 101:101 )X101
2X-RAY DIFFRACTION2( CHAIN X AND RESID 13:20 )X13 - 20
3X-RAY DIFFRACTION3( CHAIN X AND RESID 21:38 )X21 - 38
4X-RAY DIFFRACTION4( CHAIN X AND RESID 39:46 )X39 - 46
5X-RAY DIFFRACTION5( CHAIN X AND RESID 47:59 )X47 - 59
6X-RAY DIFFRACTION6( CHAIN X AND RESID 60:64 )X60 - 64
7X-RAY DIFFRACTION7( CHAIN X AND RESID 65:72 )X65 - 72
8X-RAY DIFFRACTION8( CHAIN X AND RESID 73:83 )X73 - 83

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