5U6Z

Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain

> Summary

Summary for 5U6Z

DescriptorDNA-(apurinic or apyrimidinic site) lyase (E.C.4.2.99.18)
Functional Keywordsgrf zinc finger, 3' ap endo/exonuclease, dna binding, lyase
Biological sourceXenopus laevis (African clawed frog)
Cellular locationNucleus  Q6DDT4
Total number of polymer chains1
Total molecular weight8433.98
Authors
Wallace, B.D.,Williams, R.S. (deposition date: 2016-12-09, release date: 2017-01-11)
Primary citation
Wallace, B.D.,Berman, Z.,Mueller, G.A.,Lin, Y.,Chang, T.,Andres, S.N.,Wojtaszek, J.L.,DeRose, E.F.,Appel, C.D.,London, R.E.,Yan, S.,Williams, R.S.
APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress.
Proc. Natl. Acad. Sci. U.S.A., 2016
PubMed: 28028224
DOI: 10.1073/pnas.1610011114
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.6 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.271908.9%3.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5u6z
no rotation
Molmil generated image of 5u6z
rotated about x axis by 90°
Molmil generated image of 5u6z
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA-(apurinic or apyrimidinic site) lyasepolymer758272.51
UniProt (Q6DDT4)
Xenopus laevis (African clawed frog)
ZINC IONnon-polymer65.41
SULFATE IONnon-polymer96.11
waterwater18.018

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight8272.5
Non-Polymers*Number of molecules2
Total molecular weight161.5
All*Total molecular weight8434.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.6 Å)

Cell axes90.33290.33223.105
Cell angles90.0090.0090.00
SpacegroupI 4
Resolution limits45.17 - 2.60
the highest resolution shell value2.845 - 2.585
R-factor0.2
R-work0.19480
the highest resolution shell value0.235
R-free0.24460
the highest resolution shell value0.290
RMSD bond length0.013
RMSD bond angle1.460

Data Collection Statistics

Resolution limits50.00 - 2.60
the highest resolution shell value -
Number of reflections5570
Rmerge_l_obs0.074
the highest resolution shell value0.314
Completeness97.9
Redundancy3.7
the highest resolution shell value3.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP293

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
AC14binding site for residue ZN A 101
ChainResidue
ACYS21
AHIS24
ACYS47
ACYS61

AC25binding site for residue SO4 A 102
ChainResidue
AARG31
ATHR32
ALYS34
AHOH201
AHOH207

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

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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