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- PDB-2pis: Efforts toward Expansion of the Genetic Alphabet: Structure and R... -

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Basic information

Entry
Database: PDB / ID: 2pis
TitleEfforts toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs
ComponentsDNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / nucleic acid / duplex / replication / unnatural base
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMatsuda, S. / Fillo, J.D. / Henry, A.A. / Wilkins, S.J. / Rai, P. / Dwyer, T.J. / Geierstanger, B.H. / Wemmer, D.E. / Schultz, P.G. / Spraggon, G. / Romesberg, F.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs.
Authors: Matsuda, S. / Fillo, J.D. / Henry, A.A. / Rai, P. / Wilkens, S.J. / Dwyer, T.J. / Geierstanger, B.H. / Wemmer, D.E. / Schultz, P.G. / Spraggon, G. / Romesberg, F.E.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
G: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
I: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
J: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
K: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,34318
Polymers48,19812
Non-polymers1466
Water0
1
A: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,0332
Polymers8,0332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0573
Polymers8,0332
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0824
Polymers8,0332
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1065
Polymers8,0332
Non-polymers733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
J: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,0332
Polymers8,0332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,0332
Polymers8,0332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.025, 146.025, 93.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: DNA chain
DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')


Mass: 4016.470 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Synthesized DNA
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 35% (v/v) MPD in 0.1M sodium cacodylate , pH 6.0, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3MPD12
4sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.92017, 0.9203, 0.9050
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.920171
20.92031
30.9051
ReflectionResolution: 2.8→100 Å / Num. all: 12382 / Num. obs: 12382 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 40.58
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.73 / Num. unique all: 1103 / Rsym value: 0.388 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→100 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.642 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY FOR THE CHAINS I,J AND K,L WAS EXTREMELY WEAK. THE AUTHOR STATES THAT THESE CHAINS WERE MODELED TENTATIVELY INTO THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3029 599 5.1 %RANDOM
Rwork0.2238 ---
all0.22771 11034 --
obs0.22771 11034 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2---2.53 Å20 Å2
3---5.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3144 6 0 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213552
X-RAY DIFFRACTIONr_angle_refined_deg1.1312.9975468
X-RAY DIFFRACTIONr_chiral_restr0.0530.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021608
X-RAY DIFFRACTIONr_nbd_refined0.3380.21740
X-RAY DIFFRACTIONr_nbtor_refined0.3420.21974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.30.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.25
X-RAY DIFFRACTIONr_mcbond_it2.97224
X-RAY DIFFRACTIONr_mcangle_it12.619548
X-RAY DIFFRACTIONr_scbond_it13.6285040
X-RAY DIFFRACTIONr_scangle_it16.424115340
LS refinement shellResolution: 2.8→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 39 -
Rwork0.364 620 -
obs--72.1 %

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