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- PDB-6cc3: Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium -

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Basic information

Entry
Database: PDB / ID: 6cc3
TitleCrystal structure of ykoY-mntP riboswitch chimera bound to cadmium
ComponentsRNA (101-MER)
KeywordsRNA / Riboswitch / yybP-ykoY
Function / homology: / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsBachas, S. / Ferre-D'amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.
Authors: Bachas, S.T. / Ferre-D'Amare, A.R.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (101-MER)
B: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,12932
Polymers65,3452
Non-polymers2,78430
Water81145
1
A: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,25020
Polymers32,6731
Non-polymers1,57719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,87912
Polymers32,6731
Non-polymers1,20711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.531, 68.288, 83.384
Angle α, β, γ (deg.)90.00, 97.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (101-MER)


Mass: 32672.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Magnesium Formate, 15% PEG 3350, 5mM Cadmium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.698→50 Å / Num. obs: 19403 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.63
Reflection shellResolution: 2.698→2.75 Å / Rmerge(I) obs: 0.802 / Num. unique obs: 877

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y1i
Resolution: 2.698→46.658 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 1916 9.99 %
Rwork0.1958 --
obs0.2011 19173 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.698→46.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4114 92 45 4251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024676
X-RAY DIFFRACTIONf_angle_d0.5137284
X-RAY DIFFRACTIONf_dihedral_angle_d13.9022323
X-RAY DIFFRACTIONf_chiral_restr0.026968
X-RAY DIFFRACTIONf_plane_restr0.003194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6983-2.76580.43051260.39731132X-RAY DIFFRACTION91
2.7658-2.84050.40031320.35751179X-RAY DIFFRACTION95
2.8405-2.92410.36241330.29711205X-RAY DIFFRACTION99
2.9241-3.01850.29811360.25361223X-RAY DIFFRACTION99
3.0185-3.12630.28811420.23531267X-RAY DIFFRACTION100
3.1263-3.25150.2561360.21641242X-RAY DIFFRACTION100
3.2515-3.39940.28161350.19761230X-RAY DIFFRACTION99
3.3994-3.57860.2561370.18981232X-RAY DIFFRACTION100
3.5786-3.80270.24611380.181250X-RAY DIFFRACTION99
3.8027-4.09610.22991370.16341228X-RAY DIFFRACTION100
4.0961-4.5080.20511400.15011260X-RAY DIFFRACTION100
4.508-5.15960.19681410.15541266X-RAY DIFFRACTION100
5.1596-6.49780.20311390.17461258X-RAY DIFFRACTION100
6.4978-46.66480.24231440.19211285X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.33610.86621.56791.10261.0110.9966-0.08030.01050.0912-0.16140.06790.3246-0.0084-0.25010.05650.3746-0.1573-0.00380.72790.03510.512228.7236-6.779121.8418
25.64312.1439-0.01732.60940.52070.0462-0.0204-0.34250.104-0.1788-0.13590.0157-0.0621-0.23910.13550.3546-0.0914-0.00580.58010.02270.374917.668-20.683925.9236
30.59231.0495-0.10781.80980.55874.4793-0.2310.0444-0.1374-0.1979-0.00640.29470.1259-0.17850.17520.3021-0.0120.00390.5591-0.11670.512342.1062-0.581140.4958
47.11122.0614-1.12172.55831.32665.449-0.17-0.4152-0.2432-0.1395-0.18250.1061-0.0988-0.40670.30710.5935-0.0281-0.28970.48110.10750.75196.5979-4.91127.0502
54.88832.9314-3.84372.0899-2.11595.2424-0.4260.245-0.554-0.56640.05170.22320.4286-0.03350.42620.5731-0.01680.12440.8292-0.05490.662738.5434-26.83937.4112
63.8654-0.2157-1.15865.3849-1.34945.90420.1044-0.425-0.2458-0.2415-0.4184-0.13540.54550.43170.32660.4324-0.07460.08770.7084-0.01850.413255.914-15.686313.4515
75.8601-1.714.53211.9984-3.2817.3791.5317-0.6332-0.73643.06870.8778-0.54921.0558-0.0008-2.01964.92740.20030.17181.39960.23712.64457.1034-43.2827.5869
85.4016-0.1281-0.23425.36710.06332.5375-0.63020.5277-0.2006-1.33250.06060.44940.2718-0.06980.61520.8918-0.0770.03470.9223-0.23880.642445.3134-23.3017-4.1872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:35)
2X-RAY DIFFRACTION2(chain A and resid 36:71)
3X-RAY DIFFRACTION3(chain A and resid 72:91)
4X-RAY DIFFRACTION4(chain A and resid 92:102)
5X-RAY DIFFRACTION5(chain B and resid 3:28)
6X-RAY DIFFRACTION6(chain B and resid 29:74)
7X-RAY DIFFRACTION7(chain B and resid 82:85)
8X-RAY DIFFRACTION8(chain B and resid 86:101)

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