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- PDB-6ck5: PRPP riboswitch from T. mathranii bound to PRPP -

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Basic information

Entry
Database: PDB / ID: 6ck5
TitlePRPP riboswitch from T. mathranii bound to PRPP
ComponentsPRPP riboswitch
KeywordsRNA / Riboswitch / PRPP / ykkC
Function / homology: / : / Chem-PRP / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter mathranii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKnappenberger, A.J. / Reiss, C.W. / Strobel, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Elife / Year: 2018
Title: Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.
Authors: Knappenberger, A.J. / Reiss, C.W. / Strobel, S.A.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRPP riboswitch
B: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,22735
Polymers75,3892
Non-polymers3,83833
Water93752
1
A: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,84418
Polymers37,6941
Non-polymers2,15017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,38317
Polymers37,6941
Non-polymers1,68816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.977, 89.575, 136.367
Angle α, β, γ (deg.)90.000, 96.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Refine code: _ / Auth seq-ID: 0 - 110 / Label seq-ID: 1 - 111

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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RNA chain / Sugars , 2 types, 4 molecules AB

#1: RNA chain PRPP riboswitch


Mass: 37694.297 Da / Num. of mol.: 2 / Fragment: GB residues 657680-657796 / Source method: obtained synthetically / Source: (synth.) Thermoanaerobacter mathranii (bacteria) / References: GenBank: 296841273
#5: 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.: 2 / Source method: isolated from a natural source / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 83 molecules

#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.73 Å3/Da / Density % sol: 54.99 % / Description: Crystal formed as a large, very thin plate.
Crystal growTemperature: 303.15 K / Method: microbatch / pH: 5.6
Details: 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 10 mM PRPP, mixed 2:1 with 80 mM sodium chloride, 20 mM barium chloride dihydrate, 40 mM sodium ...Details: 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 10 mM PRPP, mixed 2:1 with 80 mM sodium chloride, 20 mM barium chloride dihydrate, 40 mM sodium cacodylate trihydrate, pH 5.6, 45% v/v MPD, 12 mM spermine tetrahydrachloride. Crystals were flash-frozen without further preparation.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.798
11-H, -K, H+L20.202
ReflectionResolution: 2.5→40 Å / Num. obs: 27959 / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.118 / Χ2: 1.421 / Net I/σ(I): 9.3 / Num. measured all: 100854
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.91.06814050.1760.6331.2461.08198.9
2.54-2.593.80.95914340.2670.5751.1231.09999.3
2.59-2.643.60.93314090.1760.571.0981.04498.4
2.64-2.693.70.913490.270.5491.0591.15398.6
2.69-2.753.60.91213800.1440.5631.0780.9798.2
2.75-2.823.50.70914230.3760.4430.840.95298.3
2.82-2.893.30.59813850.6560.3870.7160.97297.7
2.89-2.963.10.38713440.8750.2570.4681.196.2
2.96-3.053.60.31314030.9670.1920.3691.12999.2
3.05-3.1540.20914240.9890.1220.2431.25699.2
3.15-3.2640.15513760.9930.090.181.35598.9
3.26-3.393.80.13714420.9940.0810.1591.47399
3.39-3.553.80.13313740.9920.080.1561.62699.3
3.55-3.733.70.11914200.9920.0720.141.78698.7
3.73-3.973.50.10113600.9930.0620.1191.74897.4
3.97-4.273.20.0814250.9950.0510.0961.80896.2
4.27-4.73.50.07213580.9940.0440.0851.98497.4
4.7-5.383.90.06314080.9930.0360.0731.85199
5.38-6.783.60.05614400.9940.0330.0652.02498.6
6.78-403.10.04814000.9980.0310.0572.10695.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
SCALEPACKdata scaling
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5T83

5t83


Resolution: 2.49→37.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.149 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1361 4.9 %RANDOM
Rwork0.2145 ---
obs0.2164 26309 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.44 Å2 / Biso mean: 78.592 Å2 / Biso min: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-51.63 Å20 Å2-31.18 Å2
2--8.9 Å2-0 Å2
3----60.53 Å2
Refinement stepCycle: final / Resolution: 2.49→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4418 75 52 4545
Biso mean--90.69 61.64 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0114985
X-RAY DIFFRACTIONr_bond_other_d0.0040.022029
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.2957764
X-RAY DIFFRACTIONr_angle_other_deg1.76934945
X-RAY DIFFRACTIONr_chiral_restr0.1150.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021089
Refine LS restraints NCS

Ens-ID: 1 / Number: 20474 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.491→2.555 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 90 -
Rwork0.363 1656 -
all-1746 -
obs--82.95 %

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