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- PDB-8crz: Crystal structure of alien DNA CTSZZPBSBSZPPBAG in a tetragonal l... -

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Basic information

Entry
Database: PDB / ID: 8crz
TitleCrystal structure of alien DNA CTSZZPBSBSZPPBAG in a tetragonal lattice
Components
  • DNA (5'-D(*CP*TP*(JSP)P*(1W5)P*(1W5)P*(1WA)P*(IGU)P*(JSP))-3')
  • DNA (5'-D(P*(IGU)P*(JSP)P*(1W5)P*(1WA)P*(1WA)P*(IGU)P*AP*G)-3')
KeywordsDNA / unnatural DNA / Alien DNA
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1939086 United States
CitationJournal: To Be Published
Title: Alien DNA visualized at high resolution in A- and B-forms
Authors: Georgiadis, M.M. / Hoshika, S. / Shukla, M. / Benner, S.A.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,0362
Polymers5,0362
Non-polymers00
Water1,42379
1
A: DNA (5'-D(*CP*TP*(JSP)P*(1W5)P*(1W5)P*(1WA)P*(IGU)P*(JSP))-3')
B: DNA (5'-D(P*(IGU)P*(JSP)P*(1W5)P*(1WA)P*(1WA)P*(IGU)P*AP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)10,0734
Polymers10,0734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)46.496, 46.496, 42.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: DNA chain DNA (5'-D(*CP*TP*(JSP)P*(1W5)P*(1W5)P*(1WA)P*(IGU)P*(JSP))-3')


Mass: 2481.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*(IGU)P*(JSP)P*(1W5)P*(1WA)P*(1WA)P*(IGU)P*AP*G)-3')


Mass: 2554.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M HEPES, pH 7.0, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.2→46.5 Å / Num. obs: 15095 / % possible obs: 99.8 % / Redundancy: 12 % / Biso Wilson estimate: 14.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.015 / Rrim(I) all: 0.05 / Net I/σ(I): 34.2 / Num. measured all: 181739 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.2212.80.20994647390.9930.060.21713.199.1
6.57-46.58.20.05110021220.9960.0190.05542.696.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→20.794 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 732 4.86 %
Rwork0.1845 14317 -
obs0.1854 15049 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.65 Å2 / Biso mean: 17.771 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.2→20.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 337 0 79 416
Biso mean---26.56 -
Num. residues----16
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.29270.2561520.2245278499
1.2927-1.42280.22361250.21812827100
1.4228-1.62860.20141470.19632822100
1.6286-2.05150.20471380.19292883100
2.0515-20.7940.1921700.1729300199

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