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- PDB-2ao5: Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal... -

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Basic information

Entry
Database: PDB / ID: 2ao5
TitleCrystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs
Components5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
KeywordsRNA / G-U base pair / RNA duplex
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUtsunomiya, R. / Suto, K. / Balasundaresan, D. / Fukamizu, A. / Kumar, P.K. / Mizuno, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.
Authors: Utsunomiya, R. / Suto, K. / Balasundaresan, D. / Fukamizu, A. / Kumar, P.K. / Mizuno, H.
History
DepositionAug 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 / struct_site
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 / _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: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
B: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
C: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
D: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1765
Polymers13,1514
Non-polymers241
Water4,504250
1
A: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
B: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6003
Polymers6,5762
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'
D: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'


Theoretical massNumber of molelcules
Total (without water)6,5762
Polymers6,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.693, 37.693, 96.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 3287.844 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: the file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, spermine, magnesium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2spermine11
3magnesium chloride11
4cacodylate11
5H2O11
6MPD12
7magnesium chloride12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 0.921 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 15349 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 36
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 19.1 / Num. unique all: 750 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 401225.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 779 5.1 %RANDOM
Rwork0.207 ---
all0.222 ---
obs0.222 15349 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.8665 Å2 / ksol: 0.289298 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2--1.47 Å20 Å2
3----2.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 852 1 250 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d6.6
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 132 5.2 %
Rwork0.279 2407 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water.paramwater.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3bru.parambru.top
X-RAY DIFFRACTION4ion.paramion.top

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