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- PDB-4xno: Crystal structure of 5'-CTTATPPPZZZATAAG -

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Basic information

Entry
Database: PDB / ID: 4xno
TitleCrystal structure of 5'-CTTATPPPZZZATAAG
ComponentsDNA (5'-D(*CP*TP*(BRU)P*AP*TP*(1WA)P*(1WA)P*(1WA)P*(1W5)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')
KeywordsDNA / A-form DNA / non-natural nucleobase pair / synthetic biology
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.985 Å
AuthorsGeorgiadis, M.M. / Singh, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111386 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2015
Title: Structural basis for a six nucleotide genetic alphabet.
Authors: Georgiadis, M.M. / Singh, I. / Kellett, W.F. / Hoshika, S. / Benner, S.A. / Richards, N.G.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Non-polymer description
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*(BRU)P*AP*TP*(1WA)P*(1WA)P*(1WA)P*(1W5)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*(BRU)P*AP*TP*(1WA)P*(1WA)P*(1WA)P*(1W5)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,2022
Polymers10,2022
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.019, 42.019, 140.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain DNA (5'-D(*CP*TP*(BRU)P*AP*TP*(1WA)P*(1WA)P*(1WA)P*(1W5)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')


Mass: 5101.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91963 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionRedundancy: 10 % / Number: 105588 / Rmerge(I) obs: 0.069 / Χ2: 1.06 / D res high: 1.98 Å / D res low: 100 Å / Num. obs: 10571 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.3710010.0410.8429.4
4.275.3710.0481.0819.7
3.734.2710.0551.41710.6
3.393.7310.0611.56410.8
3.143.3910.061.31111
2.963.1410.0711.35511
2.812.9610.1011.25311.2
2.692.8110.1281.04711.2
2.582.6910.1511.11111.2
2.492.5810.1821.02611.3
2.422.4910.2520.92511.4
2.352.4210.3170.93411.1
2.292.3510.3860.91511.1
2.232.2910.4750.88110.4
2.182.2310.5670.83710
2.132.1810.6270.919.5
2.092.1310.6430.8788.6
2.052.0910.6720.8397.7
2.012.0510.6720.8196.7
1.982.0110.7680.85.6
ReflectionResolution: 1.98→100 Å / Num. obs: 10571 / % possible obs: 99.5 % / Redundancy: 10 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.022 / Rrim(I) all: 0.072 / Χ2: 1.061 / Net I/av σ(I): 29.47 / Net I/σ(I): 20 / Num. measured all: 105588
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.60.7685090.7280.3390.8430.898.8
2.01-2.056.70.6725030.8020.2740.7280.819100
2.05-2.097.70.6725150.8410.2530.7190.839100
2.09-2.138.60.6435240.890.2260.6830.878100
2.13-2.189.50.6275160.9190.2090.6620.91100
2.18-2.23100.5675120.9470.1840.5960.837100
2.23-2.2910.40.4755290.9640.1520.4990.881100
2.29-2.3511.10.3865070.9910.1190.4040.915100
2.35-2.4211.10.3175220.9790.0980.3320.934100
2.42-2.4911.40.2525170.9850.0760.2640.925100
2.49-2.5811.30.1825310.990.0550.191.026100
2.58-2.6911.20.1515190.9910.0470.1591.111100
2.69-2.8111.20.1285440.9920.040.1351.047100
2.81-2.9611.20.1015220.9950.0310.1061.253100
2.96-3.14110.0715260.9960.0230.0741.35599.8
3.14-3.39110.065320.9960.0190.0631.311100
3.39-3.7310.80.0615490.9960.0190.0641.564100
3.73-4.2710.60.0555560.9980.0180.0581.41799.8
4.27-5.379.70.0485570.9980.0160.0511.081100
5.37-1009.40.0415810.9980.0130.0430.84292.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.985→35.227 Å / FOM work R set: 0.8106 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 481 4.75 %
Rwork0.2125 9648 -
obs0.2137 10129 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.675 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso max: 58.8 Å2 / Biso mean: 23.35 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.4472 Å20 Å20 Å2
2---2.4472 Å20 Å2
3---4.6577 Å2
Refinement stepCycle: final / Resolution: 1.985→35.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 668 0 73 741
Biso mean---29.01 -
Num. residues----32
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003746
X-RAY DIFFRACTIONf_angle_d0.8291078
X-RAY DIFFRACTIONf_chiral_restr0.03570
X-RAY DIFFRACTIONf_plane_restr0.02546
X-RAY DIFFRACTIONf_dihedral_angle_d16.672426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9848-2.2720.29741420.26462883X-RAY DIFFRACTION88
2.272-2.86230.29581880.24243275X-RAY DIFFRACTION100
2.8623-35.23230.19221510.18593490X-RAY DIFFRACTION99

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