3UGO

Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TACAAT)

> Summary

Summary for 3UGO

Related3UGP
DescriptorRNA polymerase sigma factor/DNA complex
Functional Keywordsprotein-dna complex, bacterial promoter opening, g-quartet, g-quadruplex, dna binding, transcription-dna complex, transcription/dna
Biological sourceThermus aquaticus
Total number of polymer chains3
Total molecular weight35060.68
Authors
Feklistov, A.,Darst, S.A. (deposition date: 2011-11-02, release date: 2011-12-07, modification date: 2012-03-07)
Primary citation
Feklistov, A.,Darst, S.A.
Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.
Cell(Cambridge,Mass.), 147:1257-1269, 2011
PubMed: 22136875
DOI: 10.1016/j.cell.2011.10.041
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.096 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.230602.0%8.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3ugo
no rotation
Molmil generated image of 3ugo
rotated about x axis by 90°
Molmil generated image of 3ugo
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3ugo
no rotation
Molmil generated image of 3ugo
rotated about x axis by 90°
Molmil generated image of 3ugo
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 (3ugo.pdb1.gz [38.64 KB])
Coordinate files for Biological unit (3ugo.pdb2.gz [5.47 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ARNA polymerase sigma factorpolymer24528038.61
UniProt (Q9EZJ8)
Pfam (PF00140)
Pfam (PF04539)
Pfam (PF04542)
Thermus aquaticus
B, C5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'polymer113413.32
POTASSIUM IONnon-polymer39.15
waterwater18.0131

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight34865.2
Non-Polymers*Number of molecules5
Total molecular weight195.5
All*Total molecular weight35060.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.096 Å)

Cell axes86.13486.134111.728
Cell angles90.0090.0090.00
SpacegroupP 4 2 2
Resolution limits24.48 - 2.10
the highest resolution shell value2.180 - 2.096
R-factor0.1982
R-work0.19610
the highest resolution shell value0.282
R-free0.23660
the highest resolution shell value0.317
RMSD bond length0.008
RMSD bond angle1.121

Data Collection Statistics

Resolution limits25.00 - 2.10
the highest resolution shell value -
Number of reflections25306
Rmerge_l_obs0.094
the highest resolution shell value0.712
Completeness99.9
Redundancy8.2
the highest resolution shell value8.1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP8.5295

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
A0005737cellular_componentcytoplasm
A0003677molecular_functionDNA binding
A0016987molecular_functionsigma factor activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0001123biological_processtranscription initiation from bacterial-type RNA polymerase promoter
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC116BINDING SITE FOR RESIDUE K B 12
ChainResidue
BDG9
BDG9
BDG9
BDG9
BK14
BK14
BK14
BK14
CDG11
CDG11
CDG11
CDG11
CK12
CK12
CK12
CK12

AC212BINDING SITE FOR RESIDUE K B 13
ChainResidue
BDG10
BDG10
BDG10
BDG10
BDG11
BDG11
BDG11
BDG11
BK14
BK14
BK14
BK14

AC316BINDING SITE FOR RESIDUE K B 14
ChainResidue
BDG9
BDG9
BDG9
BDG9
BDG10
BDG10
BDG10
BDG10
BK12
BK12
BK12
BK12
BK13
BK13
BK13
BK13

AC412BINDING SITE FOR RESIDUE K C 12
ChainResidue
BK12
BK12
BK12
BK12
CDG10
CDG10
CDG10
CDG10
CDG11
CDG11
CDG11
CDG11

AC58BINDING SITE FOR RESIDUE K C 13
ChainResidue
CDG9
CDG9
CDG9
CDG9
CDG10
CDG10
CDG10
CDG10

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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
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3ugo.ent.gz (45.64 KB)
Display
all (no-compress)pdb3ugo.ent (199.02 KB)
header onlypdb3ugo.ent.gz (6.61 KB)
Display
PDBx/mmCIF3ugo.cif.gz (59.3 KB)
PDBMLall3ugo.xml.gz (86.41 KB)
Display
no-atom3ugo-noatom.xml.gz (19.29 KB)
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ext-atom3ugo-extatom.xml.gz (46.04 KB)
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PDBMLplusall3ugo-plus.xml.gz (87.47 KB)
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no-atom3ugo-plus-noatom.xml.gz (20.35 KB)
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add only3ugo-add.xml.gz (1.06 KB)
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RDF3ugo.rdf.gz (36.93 KB)
Display
Structure factorsr3ugosf.ent.gz (192.33 KB)
Biological unit (PDB format)3ugo.pdb1.gz (38.64 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
3ugo.pdb2.gz (5.47 KB) (C)
*software defined assembly, 4 molecule(s) (tetrameric)
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Validation reportsPDF3ugo​_validation.pdf.gz (270.43 KB)
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PDF-full3ugo​_full​_validation.pdf.gz (275.18 KB)
Display
XML3ugo​_validation.xml.gz (12 KB)
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PNG3ugo​_multipercentile​_validation.png.gz (153.62 KB)
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SVG3ugo​_multipercentile​_validation.svg.gz (931 B)
Display
Sequence (fasta)3ugo​_seq.txt
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