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- PDB-1z79: Crystal structure of an RNA duplex containing site specific 2'-am... -

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Basic information

Entry
Database: PDB / ID: 1z79
TitleCrystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)
ComponentsRNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
KeywordsRNA / 2'-AMINE / DUPLEX / MISMATCH
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionMar 24, 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 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
A: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
C: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2834
Polymers15,2433
Non-polymers401
Water61334
1
B: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
A: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,1622
Polymers10,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,2424
Polymers10,1622
Non-polymers802
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, 122.000
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-17-

CA

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Components

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


Mass: 5081.094 Da / Num. of mol.: 3 / Source method: obtained synthetically
#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.: 34 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: MPD, Na cacodylate, spermine, calcium chloride, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Na cacodylate11
3spermine11
4calcium chloride11
5H2O11
6MPD12
7Na cacodylate12
8calcium 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 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→23 Å / Num. all: 4979 / Num. obs: 4904 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 14.29 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.1 / Net I/σ(I): 11.65
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.86 / Num. unique all: 465 / Rsym value: 0.419 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRM

1yrm


Resolution: 2.55→8.08 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 550839.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 248 5.6 %RANDOM
Rwork0.217 ---
all0.217 ---
obs0.217 4436 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6488 Å2 / ksol: 0.375414 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.13 Å22.72 Å20 Å2
2--7.13 Å20 Å2
3----14.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.55→8.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 1 34 1043
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_d1.37
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.362
X-RAY DIFFRACTIONc_scangle_it1.852.5
LS refinement shellResolution: 2.55→2.7 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 45 6.2 %
Rwork0.332 682 -
obs--99.9 %
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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