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- PDB-3npn: Structure of the s-adenosylhomocysteine riboswitch at 3.0A -

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Basic information

Entry
Database: PDB / ID: 3npn
TitleStructure of the s-adenosylhomocysteine riboswitch at 3.0A
ComponentsS-ADENOSYLHOMOCYSTEINE RIBOSWITCH
KeywordsRNA / riboswitch / S-adenosyl-homocysteine
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.792 Å
AuthorsReyes, F.E. / Edwards, A.E. / Batey, R.T.
CitationJournal: Rna / Year: 2010
Title: Structural basis for recognition of S-adenosylhomocysteine by riboswitches.
Authors: Edwards, A.L. / Reyes, F.E. / Heroux, A. / Batey, R.T.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8832
Polymers17,4991
Non-polymers3841
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.360, 105.360, 107.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain S-ADENOSYLHOMOCYSTEINE RIBOSWITCH


Mass: 17498.516 Da / Num. of mol.: 1 / Fragment: RNA / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Ralstonia solanacearum (bacteria)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 2.25 mM Spermine, 9 mM magnesium chloride, 0.9 mM spermidine, 1.8 mM Cobalt(III)hexammine chloride, 0.05 M sodium cacodylate pH 7.0, 5% (v/v) PEG 400, 20 mM iridium (III) hexammine chloride, ...Details: 2.25 mM Spermine, 9 mM magnesium chloride, 0.9 mM spermidine, 1.8 mM Cobalt(III)hexammine chloride, 0.05 M sodium cacodylate pH 7.0, 5% (v/v) PEG 400, 20 mM iridium (III) hexammine chloride, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1051 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionResolution: 2.775→29.059 Å / Num. all: 5865 / Num. obs: 5854 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rsym value: 0.123 / Net I/σ(I): 4.058
Reflection shell

Rmerge(I) obs: 0.01

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.775-2.945.70.748688521.00199.9
2.94-3.125.71.444997850.43100
3.12-3.345.7243067510.277100
3.34-3.65.72.539796980.219100
3.6-3.955.63.536716520.15499.9
3.95-4.415.65.433235960.108100
4.41-5.15.65.928855140.199.7
5.1-6.245.44.724684560.12799.9
6.24-8.835.19.718173550.054100
8.83-29.685.41110481950.05394.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.78 Å / D res low: 30 Å / FOM : 0.498 / FOM acentric: 0.518 / FOM centric: 0.332 / Reflection: 5849 / Reflection acentric: 5194 / Reflection centric: 651
Phasing dmFOM : 0.67 / FOM acentric: 0.67 / FOM centric: 0.63 / Reflection: 5850 / Reflection acentric: 5199 / Reflection centric: 651
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-30.0050.960.970.9427120170
5-80.910.920.86813680133
4-50.820.840.711005891114
3.5-40.680.70.551003898105
3-3.50.520.530.4217641611153
2.8-30.480.490.3799491876

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Processing

Software
NameVersionClassificationNB
SCALA3.3.12data scaling
PHASERphasing
RESOLVE2.14phasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.792→29.059 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.302 / WRfactor Rwork: 0.265 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.426 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.885 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.292 665 11.4 %RANDOM
Rwork0.252 ---
obs0.256 5847 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.54 Å2 / Biso mean: 78.29 Å2 / Biso min: 41.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.792→29.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1080 26 0 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211237
X-RAY DIFFRACTIONr_angle_refined_deg0.9731923
X-RAY DIFFRACTIONr_chiral_restr0.0420.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02545
X-RAY DIFFRACTIONr_mcbond_it0.0231.55
X-RAY DIFFRACTIONr_mcangle_it0.07127
X-RAY DIFFRACTIONr_scbond_it0.28131232
X-RAY DIFFRACTIONr_scangle_it0.4894.51916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.792-2.8640.325420.4936640999.756
2.864-2.9420.514530.43337643199.536
2.942-3.0260.384480.374340388100
3.026-3.1180.37530.276343396100
3.118-3.2190.298490.28432337499.465
3.219-3.3310.213370.24232636499.725
3.331-3.4550.294450.25230735399.717
3.455-3.5930.251370.27231835699.719
3.593-3.7510.263410.24129133399.7
3.751-3.930.302350.258285320100
3.93-4.1390.21330.226256289100
4.139-4.3840.32350.227256291100
4.384-4.6790.362330.228232265100
4.679-5.0440.26240.2223726399.24
5.044-5.5080.248260.22320323099.565
5.508-6.1310.332170.26193210100
6.131-7.0280.258260.257176202100
7.028-8.4840.429170.273142159100
8.484-11.5170.22670.202135142100
11.517-29.0590.26770.22779093.333
Refinement TLS params.Method: refined / Origin x: 122.7474 Å / Origin y: 68.5031 Å / Origin z: -4.2619 Å
111213212223313233
T0.2038 Å2-0.0117 Å20.0418 Å2-0.2335 Å20.0443 Å2--0.1684 Å2
L0.3356 °2-0.6233 °2-0.1711 °2-5.9404 °2-0.0541 °2--0.99 °2
S0.007 Å °0.0791 Å °0.1314 Å °-0.1905 Å °-0.1574 Å °-0.6115 Å °0.0737 Å °0.0108 Å °0.1504 Å °

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