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- PDB-4zym: Structural implications of homo-pyrimidine base pairs on the para... -

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Basic information

Entry
Database: PDB / ID: 4zym
TitleStructural implications of homo-pyrimidine base pairs on the parallel-stranded d(GAY) motif.
ComponentsDNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
KeywordsDNA / Tetraplex / homo-base pair / pyrimidine substitution.
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsTripathi, S.K. / Paukstelis, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR1149665 United States
CitationJournal: Chembiochem / Year: 2016
Title: Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded d(YGA) Motif.
Authors: Tripathi, S. / Paukstelis, P.J.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
B: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
C: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
D: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5308
Polymers13,4334
Non-polymers974
Water1086
1
A: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
B: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7654
Polymers6,7162
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
D: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7654
Polymers6,7162
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.954, 29.354, 74.731
Angle α, β, γ (deg.)90.000, 112.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain
DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3')


Mass: 3358.211 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: DNA oligonucleotide demonstrating parallel stranded DNA homoduplex.
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.26 Å3/Da / Density % sol: 45.62 % / Description: Crystals diffracted to 2.5 Angstrom
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Magnesium chloride, 5 % PEG400, 30 mM Sodium Cacodilate, 8 mM Cobalt hexamine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→69.057 Å / Num. all: 11965 / Num. obs: 4342 / % possible obs: 98.73 % / Redundancy: 2.8 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.145 / Net I/av σ(I): 6.4 / Net I/σ(I): 4.5
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 1.9 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å68.07 Å
Translation3 Å68.07 Å

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RIM

4rim


Resolution: 2.53→69.057 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 187 4.55 %Random
Rwork0.2297 3919 --
obs0.2305 4106 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 35.2971 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 2.53→69.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 826 4 6 836
Biso mean--51.33 38.92 -
Num. residues----44
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007970
X-RAY DIFFRACTIONf_angle_d0.7251493
X-RAY DIFFRACTIONf_chiral_restr0.033167
X-RAY DIFFRACTIONf_plane_restr0.00341
X-RAY DIFFRACTIONf_dihedral_angle_d34.495422
LS refinement shellResolution: 2.53→2.768 Å
RfactorNum. reflection% reflection
Rwork0.35 911 -
Rfree-187 -
obs--98.48 %

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