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- PDB-4tzx: Vibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+ -

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Basic information

Entry
Database: PDB / ID: 4tzx
TitleVibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+
ComponentsVibrio vulnificus Adenine Riboswitch
KeywordsRNA / Riboswitch / Adenine / Gene regulation
Function / homologyADENINE / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)23,04111
Polymers22,6871
Non-polymers35410
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.641, 152.839, 24.991
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
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 19, 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: 2.01→47.21 Å / Num. obs: 13466 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.1
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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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: 2.01→47.21 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1346 10 %Random
Rwork0.2239 ---
obs0.2272 13463 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 19 111 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011688
X-RAY DIFFRACTIONf_angle_d0.3492623
X-RAY DIFFRACTIONf_dihedral_angle_d11.692849
X-RAY DIFFRACTIONf_chiral_restr0.019355
X-RAY DIFFRACTIONf_plane_restr0.00272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.07760.37581350.35851205X-RAY DIFFRACTION99
2.0776-2.16070.39031270.33151146X-RAY DIFFRACTION100
2.1607-2.25910.35051350.321203X-RAY DIFFRACTION100
2.2591-2.37820.38061300.31681174X-RAY DIFFRACTION100
2.3782-2.52720.34121350.30741216X-RAY DIFFRACTION100
2.5272-2.72230.34891320.3161186X-RAY DIFFRACTION100
2.7223-2.99620.34281330.28541197X-RAY DIFFRACTION100
2.9962-3.42960.22291340.1921224X-RAY DIFFRACTION100
3.4296-4.32050.20321380.18131250X-RAY DIFFRACTION100
4.3205-47.22620.18611470.16111316X-RAY DIFFRACTION99
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)
10.91871.6499-0.17093.1141-0.39870.04030.143-0.1963-1.3512-0.4166-0.58160.61280.2776-0.3088-0.07580.4202-0.14270.04480.4759-0.07110.9931-34.4976.913-16.237
21.00431.3236-0.00592.53011.06791.18230.2948-0.2313-0.0320.238-0.2416-0.4943-0.1145-0.09420.02650.3636-0.041-0.06850.32740.10990.3293-15.21430.411-7.949
32.36110.17040.47082.9307-0.46621.6661-0.0561-0.2398-0.28990.10490.0744-0.4261-0.119-0.2683-0.0290.32510.0433-0.00610.2889-0.0270.2805-20.81319.377-10.596
41.9253-0.3107-0.24672.4826-0.49251.0515-0.009-0.1544-0.839-0.01290.003-0.40430.0762-0.1544-0.01530.3162-0.0255-0.00420.26740.01940.3893-22.2713.968-12.148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN X AND RESID 13:23 )X13 - 23
2X-RAY DIFFRACTION2( CHAIN X AND RESID 24:46 )X24 - 46
3X-RAY DIFFRACTION3( CHAIN X AND RESID 47:61 )X47 - 61
4X-RAY DIFFRACTION4( CHAIN X AND ( RESID 62:83 OR RESID 101:101 ) )X62 - 83
5X-RAY DIFFRACTION4( CHAIN X AND ( RESID 62:83 OR RESID 101:101 ) )X101

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