4J2I

Multiple crystal structures of an all-AT DNA dodecamer stabilized by weak interactions

> Summary

Summary for 4J2I

Descriptor5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'
Functional Keywordsdna, oligonucleotides, weak interactions, at-rich dna
Total number of polymer chains8
Total molecular weight29275.77
Authors
Acosta-Reyes, F.J.,Subirana, J.A.,Pous, J.,Sanchez, R.,Condom, N.,Baldini, R.,Malinina, L.,Campos, J.L. (deposition date: 2013-02-04, release date: 2014-02-05, modification date: 2015-04-15)
Primary citation
Acosta-Reyes, F.J.,Subirana, J.A.,Pous, J.,Sanchez-Giraldo, R.,Condom, N.,Baldini, R.,Malinina, L.,Campos, J.L.
Polymorphic crystal structures of an all-AT DNA dodecamer.
Biopolymers, 103:123-133, 2015
PubMed: 25257185
DOI: 10.1002/bip.22565
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.98 Å)
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Structure validation

RfreeClashscoreRSRZ outliers0.29158.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4j2i
no rotation
Molmil generated image of 4j2i
rotated about x axis by 90°
Molmil generated image of 4j2i
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, E...5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'polymer123659.58
waterwater18.017

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight29275.8
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight29275.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.98 Å)

Cell axes72.40027.945159.715
Cell angles90.00103.1090.00
SpacegroupC 1 2 1
Resolution limits26.50 - 2.98
the highest resolution shell value3.060 - 2.982
R-factor0.27031
R-work0.26963
the highest resolution shell value0.419
R-free0.28729
the highest resolution shell value0.420
RMSD bond length0.019
RMSD bond angle1.075

Data Collection Statistics

Resolution limits26.50 - 2.98
the highest resolution shell value -
Number of reflections6641
Rmerge_l_obs0.138
the highest resolution shell value0.216
Completeness99.2
Redundancy3.6
the highest resolution shell value3.6
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5286

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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Catalytic Information from CATRES

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> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4j2i.ent.gz (43.21 KB)
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all (no-compress)pdb4j2i.ent (184.94 KB)
header onlypdb4j2i.ent.gz (4.44 KB)
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PDBx/mmCIF4j2i.cif.gz (58.93 KB)
PDBMLall4j2i.xml.gz (88.26 KB)
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no-atom4j2i-noatom.xml.gz (19.69 KB)
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ext-atom4j2i-extatom.xml.gz (46.77 KB)
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PDBMLplusall4j2i-plus.xml.gz (88.48 KB)
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no-atom4j2i-plus-noatom.xml.gz (19.91 KB)
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add only4j2i-add.xml.gz (225 B)
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RDF4j2i.rdf.gz (31.99 KB)
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Structure factorsr4j2isf.ent.gz (147.23 KB)
Biological unit (PDB format)4j2i.pdb1.gz (10.58 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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4j2i.pdb2.gz (10.63 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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4j2i.pdb3.gz (10.51 KB) (E,F)
*author and software defined assembly, 2 molecule(s) (dimeric)
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4j2i.pdb4.gz (10.59 KB) (G,H)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF4j2i​_validation.pdf.gz (247.88 KB)
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PDF-full4j2i​_full​_validation.pdf.gz (248.88 KB)
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XML4j2i​_validation.xml.gz (4.94 KB)
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PNG4j2i​_multipercentile​_validation.png.gz (107.37 KB)
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SVG4j2i​_multipercentile​_validation.svg.gz (808 B)
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Sequence (fasta)4j2i​_seq.txt
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