+Open data
-Basic information
Entry | Database: PDB / ID: 5ui8 | ||||||
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Title | structure of sigmaN-holoenzyme | ||||||
Components |
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Keywords | TRANSCRIPTION / Bacterial RNA polymerase sigmaN-holoenzyme | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding ...DNA-binding transcription activator activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Escherichia coli O45:K1 (bacteria) Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.76 Å | ||||||
Authors | Darst, S.A. / Campbell, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2015 Title: TRANSCRIPTION. Structures of the RNA polymerase-sigma 54 reveal new and conserved regulatory strategies. Authors: Yang, Y. / Darbari, V.C. / Zhang, N. / Lu, D. / Glyde, R. / Wang, Y.P. / Winkelman, J.T. / Gourse, R.L. / Murakami, K.S. / Buck, M. / Zhang, X. | ||||||
History |
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Remark 0 | This entry 5UI8 reflects an alternative modeling of the structural data in r5byhSF original data ...This entry 5UI8 reflects an alternative modeling of the structural data in r5byhSF original data determined by Author: X.ZHANG,M.BUCK,V.C.DARBARI,Y.YANG,N.ZHANG,D.LU,R.GLYDE,Y.WANG,J.WINKELMAN,R.L.GOURSE,K.S.MURAKAMI |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ui8.cif.gz | 696.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ui8.ent.gz | 552 KB | Display | PDB format |
PDBx/mmJSON format | 5ui8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5ui8 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5ui8 | HTTPS FTP |
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-Related structure data
Related structure data | 5ui5C 4ljzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules GHIJK
#1: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rpoA, Z4665, ECs4160 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A7Z6, DNA-directed RNA polymerase #2: Protein | | Mass: 150804.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria) Strain: S88 / ExPEC / Gene: rpoB, ECS88_4448 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7MIX3, DNA-directed RNA polymerase #3: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rpoC, Z5561, ECs4911 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T8, DNA-directed RNA polymerase #4: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria) Strain: S88 / ExPEC / Gene: rpoZ, ECS88_4064 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7MFL0, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules M
#5: Protein | Mass: 53988.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: SAMEA2273624_03286, SM87_03359 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J4U551, UniProt: A0A087FVZ6*PLUS |
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-Non-polymers , 2 types, 3 molecules
#6: Chemical | ChemComp-MG / |
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#7: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.63 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5BYH. |
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Crystal grow | Method: vapor diffusion, sitting drop |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LJZ Resolution: 3.76→29.642 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.76→29.642 Å
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Refine LS restraints |
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LS refinement shell |
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