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- PDB-6n2v: Manganese riboswitch from Xanthmonas oryzae bound to Mn(II) -

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Basic information

Entry
Database: PDB / ID: 6n2v
TitleManganese riboswitch from Xanthmonas oryzae bound to Mn(II)
ComponentsX. oryzae Mn riboswitch optimized construct
KeywordsRNA / riboswitch / manganese
Function / homology: / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesXanthomonas oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPrice, I.R. / Ke, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116632 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118174 United States
CitationJournal: Nat Commun / Year: 2019
Title: Local-to-global signal transduction at the core of a Mn2+sensing riboswitch.
Authors: Suddala, K.C. / Price, I.R. / Dandpat, S.S. / Janecek, M. / Kuhrova, P. / Sponer, J. / Banas, P. / Ke, A. / Walter, N.G.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: X. oryzae Mn riboswitch optimized construct
B: X. oryzae Mn riboswitch optimized construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,70658
Polymers64,5622
Non-polymers2,14456
Water1267
1
A: X. oryzae Mn riboswitch optimized construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,33026
Polymers32,2811
Non-polymers1,04925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: X. oryzae Mn riboswitch optimized construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,37632
Polymers32,2811
Non-polymers1,09531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.296, 85.167, 92.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain X. oryzae Mn riboswitch optimized construct


Mass: 32281.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Xanthomonas oryzae (bacteria)

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Non-polymers , 5 types, 63 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 mM RNA in 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, mixed in a 1:1 ratio with 10% MPD, 40 mM Na Cacodylate pH 7, 12 mM spermine tetrahydrochloride, 80 mM SrCl2, 20 mM MgCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.769 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.769 Å / Relative weight: 1
ReflectionResolution: 2.85→62.64 Å / Num. obs: 15512 / % possible obs: 99.75 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.04499 / Rrim(I) all: 0.1265 / Net I/σ(I): 12.85
Reflection shellResolution: 2.85→2.952 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.932 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 1510 / CC1/2: 0.306 / Rpim(I) all: 1.131 / Rrim(I) all: 3.15 / % possible all: 99.07

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y1I

4y1i


Resolution: 2.85→62.64 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2207 2379 8.27 %
Rwork0.2092 --
obs0.2102 28774 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→62.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4278 56 7 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084787
X-RAY DIFFRACTIONf_angle_d0.4977466
X-RAY DIFFRACTIONf_dihedral_angle_d14.272372
X-RAY DIFFRACTIONf_chiral_restr0.026988
X-RAY DIFFRACTIONf_plane_restr0.002198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.90820.41241480.50031460X-RAY DIFFRACTION94
2.9082-2.97150.48021170.42751558X-RAY DIFFRACTION100
2.9715-3.04060.4411470.36481549X-RAY DIFFRACTION100
3.0406-3.11660.32511450.30261581X-RAY DIFFRACTION100
3.1166-3.20090.28051430.28121529X-RAY DIFFRACTION100
3.2009-3.29510.29641190.26871586X-RAY DIFFRACTION100
3.2951-3.40140.27391470.26171577X-RAY DIFFRACTION100
3.4014-3.5230.24331390.26161547X-RAY DIFFRACTION100
3.523-3.6640.27211420.25091576X-RAY DIFFRACTION100
3.664-3.83080.21251380.21381557X-RAY DIFFRACTION100
3.8308-4.03270.21841380.20331557X-RAY DIFFRACTION100
4.0327-4.28530.20581380.21564X-RAY DIFFRACTION100
4.2853-4.61610.2521400.18621537X-RAY DIFFRACTION100
4.6161-5.08040.17911450.17721556X-RAY DIFFRACTION99
5.0804-5.81510.17461500.17111552X-RAY DIFFRACTION100
5.8151-7.32470.21731350.16961557X-RAY DIFFRACTION100
7.3247-62.6580.15521480.15991552X-RAY DIFFRACTION99

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