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- PDB-1yzd: Crystal structure of an RNA duplex containing a site specific 2'-... -

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Basic information

Entry
Database: PDB / ID: 1yzd
TitleCrystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair
ComponentsRNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
KeywordsRNA / 2'-AMINE / DUPLEX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGherghe, C.M. / Krahn, J.M. / Weeks, K.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA.
Authors: Gherghe, C.M. / Krahn, J.M. / Weeks, K.M.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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
B: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
A: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
C: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3314
Polymers15,2913
Non-polymers401
Water52229
1
B: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
A: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2343
Polymers10,1942
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'

C: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,1942
Polymers10,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)43.000, 43.000, 121.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-19-

HOH

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Components

#1: RNA chain RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'


Mass: 5097.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, sodium cacodylate, spermidine, magnesium chloride, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3spermidine11
4magnesium chloride11
5calcium chloride11
6H2O11
7MPD12
8sodium cacodylate12
9magnesium chloride12
10calcium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→31.7 Å / Num. all: 7277 / Num. obs: 6646 / % possible obs: 91.4 % / Observed criterion σ(I): 1 / Redundancy: 21.79 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 2.18→2.28 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.37 / Num. unique all: 405 / Rsym value: 0.37 / % possible all: 57.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→8.07 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 852998.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 301 5.4 %RANDOM
Rwork0.236 ---
all0.265 5567 --
obs0.236 5556 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.0361 Å2 / ksol: 0.405429 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å22.19 Å20 Å2
2--4.45 Å20 Å2
3----8.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.35→8.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1011 1 29 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d6.9
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it1.922.5
LS refinement shellResolution: 2.35→2.49 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 38 4.4 %
Rwork0.302 824 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1C2N.PARAMC2N.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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