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- PDB-5vjb: Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substituti... -

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Basic information

Entry
Database: PDB / ID: 5vjb
TitleGuanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa
ComponentsRNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
KeywordsRNA / guanidine / riboswitch / kissing loop / hairpin
Function / homologyGUANIDINE / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.name
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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*(5BU)P*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
C: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,05413
Polymers20,9844
Non-polymers1,0709
Water19811
1
A: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0397
Polymers10,4922
Non-polymers5475
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*(5BU)P*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0156
Polymers10,4922
Non-polymers5234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.234, 60.540, 71.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5246.047 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#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.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 296.15 K / Method: microbatch / pH: 5.6
Details: 1:1 ratio of 200uM RNA in crystallization buffer (10 mM MgCl2, 10 mM KCl, 10 mM HEPES-KOH, pH 7.5, and 40 mM guanidine) and crystallization reagent (45% MPD, 50 mM MES, pH 5.6, 4 mM NaCl, 40 ...Details: 1:1 ratio of 200uM RNA in crystallization buffer (10 mM MgCl2, 10 mM KCl, 10 mM HEPES-KOH, pH 7.5, and 40 mM guanidine) and crystallization reagent (45% MPD, 50 mM MES, pH 5.6, 4 mM NaCl, 40 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: 2.1→40 Å / Num. obs: 25445 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.027 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1471.0580.5520.4271.1420.82100
2.14-2.186.90.9480.6270.3841.0240.863100
2.18-2.226.90.9160.6370.3740.990.858100
2.22-2.266.80.6810.7930.280.7370.87100
2.26-2.316.80.5680.8480.2330.6150.894100
2.31-2.376.80.4740.8910.1950.5130.896100
2.37-2.426.50.4040.9070.1710.4390.93899.9
2.42-2.496.10.3290.9440.1450.360.91999.8
2.49-2.566.40.2860.9560.1230.3110.9199.9
2.56-2.657.10.2410.9710.0970.260.96199.9
2.65-2.747.10.190.9840.0770.2050.9499.9
2.74-2.8570.1290.9930.0530.1391.00599.9
2.85-2.986.90.1010.9970.0410.1091.11999.9
2.98-3.146.60.0770.9980.0320.0841.165100
3.14-3.336.10.0610.9990.0260.0671.30799.7
3.33-3.597.30.0560.9980.0230.0611.319100
3.59-3.957.10.0480.9990.0190.0521.25799.9
3.95-4.526.90.0430.9980.0180.0471.167100
4.52-5.76.60.0370.9990.0150.041.11499.8
5.7-406.90.040.9980.0170.0431.20399.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.971 / SU B: 4.844 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.168
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 634 4.6 %RANDOM
Rwork0.2156 ---
obs0.2167 13040 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.46 Å2 / Biso mean: 40.534 Å2 / Biso min: 29.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---1.38 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1372 73 11 1456
Biso mean--60.01 36.09 -
Num. residues----64
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121601
X-RAY DIFFRACTIONr_bond_other_d0.0080.02761
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.3932458
X-RAY DIFFRACTIONr_angle_other_deg1.77531797
X-RAY DIFFRACTIONr_chiral_restr0.1060.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02824
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02396
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 36 -
Rwork0.316 757 -
all-793 -
obs--78.05 %

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