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- PDB-1mdg: An Alternating Antiparallel Octaplex in an RNA Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 1mdg
TitleAn Alternating Antiparallel Octaplex in an RNA Crystal Structure
Components5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
KeywordsRNA / tetraplex / base tetrads / base octads
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsPan, B.C. / Xiong, Y. / Shi, K. / Sundaralingam, M.
CitationJournal: Structure / Year: 2003
Title: An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction
Authors: Pan, B.C. / Xiong, Y. / Shi, K. / Sundaralingam, M.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2717
Polymers1,9951
Non-polymers2766
Water28816
1
A: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,08528
Polymers7,9804
Non-polymers1,10424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)35.956, 35.956, 38.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-101-

NA

21A-102-

NA

31A-103-

NA

41A-104-

NA

51A-105-

NA

61A-201-

NCO

71A-305-

HOH

81A-315-

HOH

DetailsThe three strands of the tetraplex is generated by the four fold axis

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Components

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


Mass: 1995.093 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.54 Å3/Da / Density % sol: 20.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: MPD, MgCl2, Cobalt(III)hexammine, ethidine bromide, sodium cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl211
3Cobalt(III)hexammine11
4ethidine bromide11
5sodium cacodylate11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMRNA1drop
240 mMsodium cacodylate1droppH6.6
35 mM1dropMgCl2
41 mMcobalt hexammine chloride1drop
51 mMethidine bromide1drop
62 %(v/v)MPD1drop
715 %MPD1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9195, 0.9192, 0.800
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: May 31, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91951
20.91921
30.81
ReflectionResolution: 1.5→30 Å / Num. all: 3807 / Num. obs: 3800 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 41.7 % / Rsym value: 0.056
Reflection shellResolution: 1.5→1.55 Å / Num. unique all: 364 / Rsym value: 0.309 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 158438 / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Isotropic thermal model: isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 381 -random
Rwork0.172 ---
all-3821 --
obs-3763 98.5 %-
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 128 12 16 156
Refinement
*PLUS
Highest resolution: 1.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg4.6

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