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

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Basic information

Entry
Database: PDB / ID: 1yrm
TitleCrystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch
ComponentsDNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
KeywordsRNA / 2'-AMINE / DUPLEX / MISMATCH
Function / homologySTRONTIUM ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,4195
Polymers15,2433
Non-polymers1752
Water90150
1
A: DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2503
Polymers10,1622
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,3374
Polymers10,1622
Non-polymers1752
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, 122.500
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-

SR

21A-51-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(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-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 42.65 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, cacodylate, spermidine, strontium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2spermidine11
3strontium chloride11
4cacodylateCacodylic acid11
5strontium chloride12
6MPD12
7cacodylateCacodylic acid12

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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: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→21.5 Å / Num. all: 5573 / Num. obs: 5305 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.09 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.041 / Net I/σ(I): 17.19
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.77 / Num. unique all: 395 / Rsym value: 0.187 / % possible all: 75.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY AR0002

Resolution: 2.5→7.98 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 696091 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 253 5.4 %RANDOM
Rwork0.234 ---
all0.234 4649 --
obs0.234 4649 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6756 Å2 / ksol: 0.228829 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.26 Å25.47 Å20 Å2
2--6.26 Å20 Å2
3----12.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 2 50 1060
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_d7.3
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it0.362
X-RAY DIFFRACTIONc_scangle_it0.622.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 43 6.2 %
Rwork0.335 648 -
obs--90.2 %
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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