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- PDB-4b8d: TENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA -

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Basic information

Entry
Database: PDB / ID: 4b8d
TitleTENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA
Components
  • 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
  • 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
  • 5'-D(*GP*GP*CP*TP*GP*CP)-3'
  • 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'
KeywordsDNA / ROLLING CIRCLE AMPLIFICATION / DNA ORIGAMI
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.79 Å
AuthorsDucani, C. / Kaul, C.D. / Moche, M. / Shih, W.M. / Hogberg, B.
CitationJournal: Nat.Methods / Year: 2013
Title: Enzymatic Production of 'Monoclonal Stoichiometric' Single-Stranded DNA Oligonucleotides
Authors: Ducani, C. / Kaul, C.D. / Moche, M. / Shih, W.M. / Hogberg, B.
History
DepositionAug 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_symm_contact ...pdbx_database_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'

A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'

A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.437, 106.437, 95.154
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: DNA chain 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'


Mass: 6457.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#2: DNA chain 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'


Mass: 2082.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#3: DNA chain 5'-D(*GP*GP*CP*TP*GP*CP)-3'


Mass: 1825.216 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#4: DNA chain 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'


Mass: 2432.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
Compound detailsTHE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD ...THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP *CP*A)-3' (#2) 1 STRAND 5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* CP*G)-3' (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), 7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS OF #3 STRAND (CHAINS C AND D). THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (2_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A.

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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: 8.59 Å3/Da / Density % sol: 85.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 4.79→42.3 Å / Num. obs: 1980 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 273.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 4.79→5.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GBI

3gbi


Resolution: 4.79→42.28 Å / Cor.coef. Fo:Fc: 0.8711 / Cor.coef. Fo:Fc free: 0.8744 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.644
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 185 9.34 %RANDOM
Rwork0.1848 ---
obs0.1872 1980 99.6 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-65.6198 Å20 Å20 Å2
2--65.6198 Å20 Å2
3----131.2396 Å2
Refine analyzeLuzzati coordinate error obs: 0.672 Å
Refinement stepCycle: LAST / Resolution: 4.79→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 863 0 0 863
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01988HARMONIC2
X-RAY DIFFRACTIONt_angle_deg2.461517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes42HARMONIC5
X-RAY DIFFRACTIONt_it988HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion29.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion130SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1014SEMIHARMONIC4
LS refinement shellResolution: 4.79→5.36 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2933 49 8.78 %
Rwork0.2433 509 -
all0.2475 558 -
obs--99.6 %

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