5CY2

Tn3 resolvase - site III complex crystal form II

> Summary

Summary for 5CY2

DescriptorTransposon Tn3 resolvase/DNA Complex
Functional Keywordsdna recombinase repressor dna binding protein phosphotransferase, recombination-dna complex, recombination/dna
Biological sourceEscherichia coli
Total number of polymer chains8
Total molecular weight119382
Authors
Montano, P.S.,Rice, P.A. (deposition date: 2015-07-30, release date: 2017-01-11)
Primary citation
Montano, S.P.,Rice, P.A.
Structures of resolvase - accessory site complexes
To Be Published,
Experimental method
X-RAY DIFFRACTION (4 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.24460.4%0.7%0.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5cy2
no rotation
Molmil generated image of 5cy2
rotated about x axis by 90°
Molmil generated image of 5cy2
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5cy2
no rotation
Molmil generated image of 5cy2
rotated about x axis by 90°
Molmil generated image of 5cy2
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5cy2.pdb1.gz [234.09 KB])
Coordinate files for Biological unit (5cy2.pdb2.gz [235.15 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, E, FTransposon Tn3 resolvasepolymer19221551.64
UniProt (P0ADI2)
Pfam (PF00239)
Pfam (PF02796)
Escherichia coli
C, GDNA (27-MER)polymer278320.42
D, HDNA (27-MER)polymer278267.42

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight119382.0
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight119382.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (4 Å)

Cell axes144.900151.920106.140
Cell angles90.0099.8590.00
SpacegroupC 1 2 1
Resolution limits49.25 - 4.00
the highest resolution shell value4.211 - 4.000
R-factor0.2094
R-work0.20720
the highest resolution shell value0.331
R-free0.24980
the highest resolution shell value0.362
RMSD bond length0.010
RMSD bond angle1.090

Data Collection Statistics

Resolution limits100.00 - 4.00
the highest resolution shell value -
Number of reflections19099
Completeness99.5
Redundancy3.5
the highest resolution shell value2.6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5290

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

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
SWS_FT_FI11O-(5'-phospho-DNA)-serine intermediate. {ECO:0000255|PROSITE-ProRule:PRU01072}.
ChainResidueDetails
ASER10

SWS_FT_FI21H-T-H motif. {ECO:0000255}.
ChainResidueDetails
AALA161-GLU180

SWS_FT_FI31O-(5'-phospho-DNA)-serine intermediate. {ECO:0000255|PROSITE-ProRule:PRU01072}.
ChainResidueDetails
BSER10

SWS_FT_FI41H-T-H motif. {ECO:0000255}.
ChainResidueDetails
BALA161-GLU180

SWS_FT_FI51O-(5'-phospho-DNA)-serine intermediate. {ECO:0000255|PROSITE-ProRule:PRU01072}.
ChainResidueDetails
ESER10

SWS_FT_FI61H-T-H motif. {ECO:0000255}.
ChainResidueDetails
EALA161-GLU180

SWS_FT_FI71O-(5'-phospho-DNA)-serine intermediate. {ECO:0000255|PROSITE-ProRule:PRU01072}.
ChainResidueDetails
FSER10

SWS_FT_FI81H-T-H motif. {ECO:0000255}.
ChainResidueDetails
FALA161-GLU180

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5cy2.ent.gz (475 KB)
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all (no-compress)pdb5cy2.ent (1.81 MB)
header onlypdb5cy2.ent.gz (9.78 KB)
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PDBx/mmCIF5cy2.cif.gz (559.83 KB)
PDBMLall5cy2.xml.gz (737.72 KB)
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no-atom5cy2-noatom.xml.gz (39.96 KB)
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ext-atom5cy2-extatom.xml.gz (306.82 KB)
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PDBMLplusall5cy2-plus.xml.gz (738.96 KB)
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no-atom5cy2-plus-noatom.xml.gz (41.21 KB)
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add only5cy2-add.xml.gz (1.25 KB)
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RDF5cy2.rdf.gz (78.74 KB)
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Structure factorsr5cy2sf.ent.gz (276.87 KB)
Biological unit (PDB format)5cy2.pdb1.gz (234.09 KB) (A,B,C,D)
*author and software defined assembly, 4 molecule(s) (tetrameric)
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5cy2.pdb2.gz (235.15 KB) (E,F,G,H)
*author and software defined assembly, 4 molecule(s) (tetrameric)
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Validation reportsPDF5cy2​_validation.pdf.gz (293.29 KB)
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PDF-full5cy2​_full​_validation.pdf.gz (301.09 KB)
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XML5cy2​_validation.xml.gz (27.45 KB)
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PNG5cy2​_multipercentile​_validation.png.gz (157.53 KB)
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SVG5cy2​_multipercentile​_validation.svg.gz (944 B)
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Sequence (fasta)5cy2​_seq.txt
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