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- PDB-1l3z: Crystal Structure Analysis of an RNA Heptamer -

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Basic information

Entry
Database: PDB / ID: 1l3z
TitleCrystal Structure Analysis of an RNA Heptamer
Components5'-R(*GP*UP*AP*UP*AP*CP*A)-3'
KeywordsRNA
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsShi, K. / Pan, B. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs
Authors: Shi, K. / Pan, B. / Sundaralingam, M.
History
DepositionMar 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Feb 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.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_symmetry / _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_symmetry / _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*UP*AP*UP*AP*CP*A)-3'
B: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4343
Polymers4,4112
Non-polymers231
Water70339
1
A: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,4574
Polymers4,4112
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
2
B: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3'

B: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)4,4112
Polymers4,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Unit cell
Length a, b, c (Å)25.740, 106.580, 30.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-129-

HOH

31A-202-

HOH

41B-201-

HOH

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Components

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


Mass: 2205.379 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growpH: 7 / Details: MPD, CaCl2, Cacodylate buffer, pH7.0
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2CaCl211
3Cacodylate buffer11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMoligonucleotide1dropsingle strand concentration
240 mMsodium cacodylate1droppH7.0
324 mM1dropCaCl2
42 %(v/v)MPD1drop
540 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 22206 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2
Reflection shellResolution: 2.01→2.13 Å
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 2840 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.01→20 Å / Rfactor Rfree error: 0.014 / Data cutoff high rms absF: 545644.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 259 9.2 %RANDOM
Rwork0.18 ---
obs0.18 2808 92.5 %-
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å20 Å2
2---2.95 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 292 1 39 332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d10.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.332
X-RAY DIFFRACTIONc_scangle_it1.852.5
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 35 9.6 %
Rwork0.245 329 -
obs--74 %
Refinement
*PLUS
Rfactor Rfree: 0.185 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg10.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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