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- PDB-4xw7: Crystal structure of the ZMP riboswitch at 2.50 angstrom -

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Basic information

Entry
Database: PDB / ID: 4xw7
TitleCrystal structure of the ZMP riboswitch at 2.50 angstrom
Componentspfl RNA
KeywordsRNA / Riboswitch / ZMP / AICAR
Function / homologyAMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesActinomyces odontolyticus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsTrausch, J.J. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073850 United States
CitationJournal: Chem.Biol. / Year: 2015
Title: Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.
Authors: Trausch, J.J. / Marcano-Velazquez, J.G. / Matyjasik, M.M. / Batey, R.T.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pfl RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,61419
Polymers20,7821
Non-polymers1,83218
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.160, 40.160, 234.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-113-

MG

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Components

#1: RNA chain pfl RNA


Mass: 20782.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces odontolyticus (bacteria) / Production host: Enterobacteria phage T7 (virus)
#2: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N4O8P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H18IrN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop
Details: PEG 8K, ammonium acetate, Magnesium acetate, cacodylate
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30.53 Å / Num. obs: 7349 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 4.2
Reflection shellHighest resolution: 2.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 725 / CC1/2: 0.979 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CrystalCleardata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→25.565 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2735 720 10.08 %
Rwork0.2495 --
obs0.252 7144 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→25.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1379 63 31 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011590
X-RAY DIFFRACTIONf_angle_d0.4212502
X-RAY DIFFRACTIONf_dihedral_angle_d12.439767
X-RAY DIFFRACTIONf_chiral_restr0.021324
X-RAY DIFFRACTIONf_plane_restr0.00266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.6930.44341280.38131158X-RAY DIFFRACTION91
2.693-2.96360.41981390.35881228X-RAY DIFFRACTION97
2.9636-3.39160.26861430.26281276X-RAY DIFFRACTION98
3.3916-4.26980.21241490.20961326X-RAY DIFFRACTION100
4.2698-25.56680.24461610.2091436X-RAY DIFFRACTION100

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