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- PDB-6dlq: PRPP Riboswitch bound to PRPP, manganese chloride soaked structure -

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Basic information

Entry
Database: PDB / ID: 6dlq
TitlePRPP Riboswitch bound to PRPP, manganese chloride soaked structure
ComponentsPRPP Riboswitch
KeywordsRNA / riboswitch / non-coding / yKKC
Function / homology: / : / Chem-PRP / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSyntrophothermus lipocalidus DSM 12680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsPeselis, A. / Serganov, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM119357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM88118 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.
Authors: Peselis, A. / Serganov, A.
History
DepositionJun 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRPP Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,08319
Polymers34,9031
Non-polymers1,18018
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.321, 90.506, 73.482
Angle α, β, γ (deg.)90.00, 122.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / Sugars , 2 types, 2 molecules A

#1: RNA chain PRPP Riboswitch


Mass: 34902.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophothermus lipocalidus DSM 12680 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 25 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NH4-acetate, 0.1 M HEPES-KOH pH 7.4, and 45% 2-methyl-2,4-pentanediol (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 21504 / % possible obs: 98.4 % / Redundancy: 5.1 % / CC1/2: 0.987 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Net I/σ(I): 28.1
Reflection shellResolution: 2.8→20 Å / Rmerge(I) obs: 0.518 / Rpim(I) all: 0.3269

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Processing

Software
NameVersionClassification
REFMAC(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→20 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.58
RfactorNum. reflection% reflection
Rfree0.2542 2188 10.17 %
Rwork0.2258 --
obs0.2287 21504 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2310 39 8 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022606
X-RAY DIFFRACTIONf_angle_d0.584070
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241298
X-RAY DIFFRACTIONf_chiral_restr0.026537
X-RAY DIFFRACTIONf_plane_restr0.003108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7977-2.85840.60851020.5863934X-RAY DIFFRACTION73
2.8584-2.92470.42061430.45361084X-RAY DIFFRACTION86
2.9247-2.99760.3871180.39041134X-RAY DIFFRACTION89
2.9976-3.07830.34541220.35221239X-RAY DIFFRACTION93
3.0783-3.16860.33921590.31891143X-RAY DIFFRACTION93
3.1686-3.27040.34551160.28871271X-RAY DIFFRACTION96
3.2704-3.38680.24511650.25711194X-RAY DIFFRACTION96
3.3868-3.52170.29091390.25831257X-RAY DIFFRACTION98
3.5217-3.6810.32931350.25061285X-RAY DIFFRACTION98
3.681-3.87380.25121380.22671264X-RAY DIFFRACTION99
3.8738-4.11450.22991450.2131250X-RAY DIFFRACTION99
4.1145-4.4290.22881450.20331228X-RAY DIFFRACTION98
4.429-4.86880.2121360.2031287X-RAY DIFFRACTION98
4.8688-5.56010.1991540.17261230X-RAY DIFFRACTION98
5.5601-6.95560.22281370.18941281X-RAY DIFFRACTION98
6.9556-19.98380.21811340.17771235X-RAY DIFFRACTION96

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