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- PDB-5vj9: Guanidine-II riboswitch P2 hairpin dimer from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5vj9
TitleGuanidine-II riboswitch P2 hairpin dimer from Pseudomonas aeruginosa
ComponentsRNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
KeywordsRNA / Kissing stem-loop / hairpin / dimer / guanidine
Function / homologyGUANIDINE / : / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsReiss, 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: RNA / Year: 2017
Title: Structural basis for ligand binding to the guanidine-II riboswitch.
Authors: Reiss, C.W. / Strobel, S.A.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
C: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,98015
Polymers20,6694
Non-polymers1,31111
Water5,062281
1
A: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0848
Polymers10,3342
Non-polymers7496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8967
Polymers10,3342
Non-polymers5625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.252, 60.664, 72.308
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*UP*GP*C)-3')


Mass: 5167.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

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Non-polymers , 5 types, 292 molecules

#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.67 Å3/Da / Density % sol: 53.87 % / Description: Crystals grew as rectangular prisms
Crystal growTemperature: 296.15 K / Method: microbatch / pH: 5
Details: 40% MPD, 50 mM Na-acetate, pH 5.0, 12 mM NaCl, 80 mM KCl, and 12 mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9193 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 1.57→40 Å / Num. obs: 31438 / % possible obs: 99.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.055 / Χ2: 0.977 / Net I/σ(I): 7.6 / Num. measured all: 361260
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.66.91.01615140.5650.4021.0971.05298.8
1.6-1.6380.95515350.7280.3511.0211.05798.8
1.63-1.669.30.76715440.8780.2610.8121.00599.8
1.66-1.6911.50.68815510.9170.210.720.99199.9
1.69-1.7312.40.61815430.9390.1810.6440.972100
1.73-1.7712.40.61215420.890.180.6390.913100
1.77-1.8112.40.53615680.9080.1580.560.88799.9
1.81-1.8612.10.47615600.9210.1420.4970.87399.9
1.86-1.92110.37115560.9450.1160.3890.85699.9
1.92-1.9812.10.31115470.9710.0920.3240.822100
1.98-2.0512.70.22715660.9880.0660.2360.81699.9
2.05-2.1312.50.18115670.9910.0530.1890.837100
2.13-2.2312.30.13815530.9940.0410.1440.82199.8
2.23-2.3510.90.10515900.9960.0330.110.86699.8
2.35-2.4912.80.08115760.9980.0230.0840.869100
2.49-2.6812.70.06715830.9980.0190.0690.93100
2.68-2.95120.046159110.0140.0481.01899.8
2.95-3.3812.10.034160210.010.0361.26899.8
3.38-4.2612.20.031162710.0090.0331.40599.9
4.26-4011.20.03117230.9990.010.0331.32299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.37 Å34.12 Å
Translation5.37 Å34.12 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→40 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.2322 / WRfactor Rwork: 0.1891 / FOM work R set: 0.7925 / SU B: 2.252 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0843 / SU Rfree: 0.0901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1495 4.8 %RANDOM
Rwork0.1924 ---
obs0.1943 29890 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.27 Å2 / Biso mean: 30.604 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---1 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.57→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1368 78 281 1727
Biso mean--44.96 43.1 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0111595
X-RAY DIFFRACTIONr_bond_other_d0.0070.02770
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.3032442
X-RAY DIFFRACTIONr_angle_other_deg1.71131816
X-RAY DIFFRACTIONr_chiral_restr0.0840.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02400
LS refinement shellResolution: 1.571→1.612 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 108 -
Rwork0.399 2095 -
all-2203 -
obs--96.79 %

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