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- PDB-6ck4: G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp -

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Basic information

Entry
Database: PDB / ID: 6ck4
TitleG96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp
ComponentsPRPP riboswitch
KeywordsRNA / Riboswitch / ykkC / PRPP / ppGpp
Function / homologyGUANOSINE-5',3'-TETRAPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter mathranii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.097 Å
AuthorsReiss, C.W. / Knappenberger, A.J. / 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
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 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
C: PRPP riboswitch
D: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,11449
Polymers150,7134
Non-polymers4,40145
Water37821
1
A: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22915
Polymers37,6781
Non-polymers1,55114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5119
Polymers37,6781
Non-polymers8328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,73113
Polymers37,6781
Non-polymers1,05312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64312
Polymers37,6781
Non-polymers96511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.252, 62.147, 125.909
Angle α, β, γ (deg.)91.180, 89.610, 101.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name P or name...
21(chain B and ((resid 1 and (name P or name...
31(chain C and ((resid 1 and (name P or name...
41(chain D and (resid 1 through 37 or (resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 1 and (name P or name...A1
121(chain A and ((resid 1 and (name P or name...A0 - 112
131(chain A and ((resid 1 and (name P or name...A0 - 112
141(chain A and ((resid 1 and (name P or name...A0 - 112
151(chain A and ((resid 1 and (name P or name...A0 - 112
161(chain A and ((resid 1 and (name P or name...A0 - 112
171(chain A and ((resid 1 and (name P or name...A0 - 112
181(chain A and ((resid 1 and (name P or name...A0 - 112
191(chain A and ((resid 1 and (name P or name...A0 - 112
1101(chain A and ((resid 1 and (name P or name...A0 - 112
1111(chain A and ((resid 1 and (name P or name...A0 - 112
1121(chain A and ((resid 1 and (name P or name...A0 - 112
211(chain B and ((resid 1 and (name P or name...B1
221(chain B and ((resid 1 and (name P or name...B0 - 111
231(chain B and ((resid 1 and (name P or name...B0 - 111
241(chain B and ((resid 1 and (name P or name...B0 - 111
251(chain B and ((resid 1 and (name P or name...B0 - 111
261(chain B and ((resid 1 and (name P or name...B0 - 111
271(chain B and ((resid 1 and (name P or name...B0 - 111
281(chain B and ((resid 1 and (name P or name...B0 - 111
291(chain B and ((resid 1 and (name P or name...B0 - 111
2101(chain B and ((resid 1 and (name P or name...B0 - 111
2111(chain B and ((resid 1 and (name P or name...B0 - 111
2121(chain B and ((resid 1 and (name P or name...B0 - 111
311(chain C and ((resid 1 and (name P or name...C1
321(chain C and ((resid 1 and (name P or name...C0 - 111
331(chain C and ((resid 1 and (name P or name...C0 - 111
341(chain C and ((resid 1 and (name P or name...C0 - 111
351(chain C and ((resid 1 and (name P or name...C0 - 111
361(chain C and ((resid 1 and (name P or name...C0 - 111
371(chain C and ((resid 1 and (name P or name...C0 - 111
381(chain C and ((resid 1 and (name P or name...C0 - 111
391(chain C and ((resid 1 and (name P or name...C0 - 111
3101(chain C and ((resid 1 and (name P or name...C0 - 111
3111(chain C and ((resid 1 and (name P or name...C0 - 111
3121(chain C and ((resid 1 and (name P or name...C0 - 111
411(chain D and (resid 1 through 37 or (resid 38...D1 - 37
421(chain D and (resid 1 through 37 or (resid 38...D38
431(chain D and (resid 1 through 37 or (resid 38...D0 - 115
441(chain D and (resid 1 through 37 or (resid 38...D0 - 115
451(chain D and (resid 1 through 37 or (resid 38...D0 - 115
461(chain D and (resid 1 through 37 or (resid 38...D0 - 115
471(chain D and (resid 1 through 37 or (resid 38...D0 - 115
481(chain D and (resid 1 through 37 or (resid 38...D0 - 115
491(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4101(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4111(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4121(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4131(chain D and (resid 1 through 37 or (resid 38...D0 - 115

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
PRPP riboswitch


Mass: 37678.297 Da / Num. of mol.: 4 / Fragment: GB residues 657680-657796 / Mutation: G96A / Source method: obtained synthetically / Source: (synth.) Thermoanaerobacter mathranii (bacteria) / References: GenBank: 296841273

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Non-polymers , 6 types, 66 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.7 Å3/Da / Density % sol: 54.47 % / Description: Crystals formed as thin plates.
Crystal growTemperature: 296.15 K / Method: microbatch / pH: 7.5
Details: 1 uL 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 1 mM ppGpp, mixed with 0.8 uL 80 mM sodium chloride, 40 mM sodium cacodylate, pH 7.0, 30% MPD, 12 mM spermine

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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: Dec 10, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.097→40 Å / Num. obs: 26741 / % possible obs: 93.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 97.77 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.082 / Rrim(I) all: 0.13 / Χ2: 0.927 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.152.11.22213090.2531.0261.6040.91294.7
3.15-3.212.31.13313420.3650.951.4870.95194.3
3.21-3.272.31.1213560.2980.9391.471.00794.6
3.27-3.342.41.06213640.4990.8811.3881.00494.7
3.34-3.412.30.90513410.5780.7521.1831.01795.3
3.41-3.492.30.92913860.4610.7791.2190.98594.5
3.49-3.582.30.79513620.6060.6651.0421.05695.7
3.58-3.682.20.75313430.6730.6380.9921.01594.5
3.68-3.782.20.62313500.8230.5220.8180.91394.7
3.78-3.912.20.60113410.7550.5060.790.98993
3.91-4.042.20.61213300.7720.5130.8030.97893.5
4.04-4.212.10.5113170.7410.430.6710.9892.9
4.21-4.420.41512630.7730.3470.5450.93487.6
4.4-4.632.10.27811980.8940.2340.3660.90285.1
4.63-4.922.30.2313780.8770.1910.3010.87895.8
4.92-5.32.40.14413850.9490.120.1890.87596.3
5.3-5.832.30.10513750.9730.0870.1370.90395.8
5.83-6.672.30.07513770.9870.0620.0980.8695.8
6.67-8.392.10.0412920.9960.0330.0520.71991
8.39-402.30.03213320.9920.0260.0420.64393.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å36.54 Å
Translation3.1 Å36.54 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.7.17phasing
PHENIX1.12-2829refinement
REFMAC5refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.097→36.539 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 43.12
RfactorNum. reflection% reflection
Rfree0.3041 1263 4.74 %
Rwork0.2484 --
obs0.2509 26642 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 352.48 Å2 / Biso mean: 144.6331 Å2 / Biso min: 34.84 Å2
Refinement stepCycle: final / Resolution: 3.097→36.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8829 191 21 9041
Biso mean--120.91 95.64 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01810075
X-RAY DIFFRACTIONf_angle_d1.85215597
X-RAY DIFFRACTIONf_chiral_restr0.1372082
X-RAY DIFFRACTIONf_plane_restr0.01412
X-RAY DIFFRACTIONf_dihedral_angle_d19.5565005
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4438X-RAY DIFFRACTION10.364TORSIONAL
12B4438X-RAY DIFFRACTION10.364TORSIONAL
13C4438X-RAY DIFFRACTION10.364TORSIONAL
14D4438X-RAY DIFFRACTION10.364TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0965-3.22050.42851250.41222671279689
3.2205-3.36690.44071410.41032882302394
3.3669-3.54430.42051400.3942895303595
3.5443-3.76620.40071770.35882826300394
3.7662-4.05660.40951460.3262843298993
4.0566-4.46420.33481250.28692696282189
4.4642-5.10870.30351220.22262833295593
5.1087-6.43070.25561440.2052922306696
6.4307-36.54190.23231430.17592811295492

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