4C5X

Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethylcystosine Modification

> Summary

Summary for 4C5X

Related4C63 4C64
Descriptor5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3'
Functional Keywordsdna, cytosine modification
Biological sourceSYNTHETIC CONSTRUCT
Total number of polymer chains2
Total molecular weight7411.2
Authors
McDonough, M.,El-Sagheer, A.H.,Brown, T.,Schofield, C.J. (deposition date: 2013-09-16, release date: 2013-10-02, modification date: 2014-02-12)
Primary citation
Lercher, L.,Mcdonough, M.A.,El-Sagheer, A.H.,Thalhammer, A.,Kriaucionis, S.,Brown, T.,Schofield, C.J.
Structural Insights Into How 5-Hydroxymethylation Influences Transcription Factor Binding.
Chem.Commun.(Camb.), 50:1794-, 2014
PubMed: 24287551
DOI: 10.1039/C3CC48151D
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.3 Å)
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Structure validation

RfreeClashscoreRSRZ outliers0.16630MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4c5x
no rotation
Molmil generated image of 4c5x
rotated about x axis by 90°
Molmil generated image of 4c5x
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'polymer123693.42
SYNTHETIC CONSTRUCT
MAGNESIUM IONnon-polymer24.31
waterwater18.0136

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight7386.9
Non-Polymers*Number of molecules1
Total molecular weight24.3
All*Total molecular weight7411.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.3 Å)
Cell axes25.30040.27064.880
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits34.20 - 1.30
the highest resolution shell value1.321 - 1.300
R-factor0.1452
R-work0.14210
the highest resolution shell value0.195
R-free0.17340
the highest resolution shell value0.226
RMSD bond length0.022
RMSD bond angle2.486

Data Collection Statistics

Resolution limits34.22 - 1.21
the highest resolution shell value -
Number of reflections19814
Rmerge_l_obs0.020
the highest resolution shell value0.520
Completeness95.8
Redundancy5.3
the highest resolution shell value4.3
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
17.5

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
AC16BINDING SITE FOR RESIDUE MG A 101
ChainResidue
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

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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

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

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Catalytic Information from CATRES

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> Sequence Neighbor

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