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- PDB-4lup: Crystal structure of the complex formed by region of E. coli sigm... -

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Basic information

Entry
Database: PDB / ID: 4lup
TitleCrystal structure of the complex formed by region of E. coli sigmaE bound to its -10 element non template strand
Components
  • RNA polymerase sigma factor
  • region 2 of sigmaE of E. coli
KeywordsTRANSCRIPTION/DNA / ECF sigma factor region 2 / Transcription redirection / -10 promoter element / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain ...RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / RNA polymerase sigma factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsCampagne, S. / Marsh, M.E. / Vorholt, J.A.V. / Allain, F.H.-T. / Capitani, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for -10 promoter element melting by environmentally induced sigma factors.
Authors: Campagne, S. / Marsh, M.E. / Capitani, G. / Vorholt, J.A. / Allain, F.H.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor
C: RNA polymerase sigma factor
B: region 2 of sigmaE of E. coli
D: region 2 of sigmaE of E. coli
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8095
Polymers28,7474
Non-polymers621
Water3,729207
1
A: RNA polymerase sigma factor
B: region 2 of sigmaE of E. coli
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4353
Polymers14,3732
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA polymerase sigma factor
D: region 2 of sigmaE of E. coli


Theoretical massNumber of molelcules
Total (without water)14,3732
Polymers14,3732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.050, 36.480, 73.370
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA polymerase sigma factor


Mass: 12251.906 Da / Num. of mol.: 2 / Fragment: UNP residues 3-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoE, BN17_18601, ECs3439, LF82_1962 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P6M2
#2: DNA chain region 2 of sigmaE of E. coli


Mass: 2121.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligonucleotide synthetically generated
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / pH: 6.5
Details: The complex crystallized spontaneously at a concentration of 0.5 mM in the NMR buffer (10 mM Na-Phosphate buffer pH 6.5, 50 mM NaCl), BATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: PSI PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2013
RadiationMonochromator: FIXED EXIT DOUBLE, CHANNEL DCM MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→35.075 Å / Num. obs: 64851 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 28.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.2-1.30.6574.381100
1.3-1.40.4066.911100
1.4-1.50.23211.111100
1.5-1.80.124.811100
1.8-20.05643.471100
2-2.50.03762.51100
2.5-30.02874.861100
3-40.02494.541100
4-50.022101.051100
5-60.02294.681100
6-80.02191.41100
8-100.01894.181100
10-200.01886.63199.1
20-300.01860.431100
30-35.0750.01636.46150

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
DA+data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MAP
Resolution: 1.2→35.075 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.09 / σ(F): 1.36 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1648 972 1.5 %
Rwork0.1471 --
obs0.1474 64837 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.3977 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 268 4 207 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061870
X-RAY DIFFRACTIONf_angle_d0.9942594
X-RAY DIFFRACTIONf_dihedral_angle_d16.387711
X-RAY DIFFRACTIONf_chiral_restr0.066293
X-RAY DIFFRACTIONf_plane_restr0.005288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.26330.19131380.15399087X-RAY DIFFRACTION100
1.2633-1.34240.17421380.13069044X-RAY DIFFRACTION100
1.3424-1.44610.17361380.11969082X-RAY DIFFRACTION100
1.4461-1.59160.12881380.10449082X-RAY DIFFRACTION100
1.5916-1.82190.14041380.11519113X-RAY DIFFRACTION100
1.8219-2.29540.14021400.14599153X-RAY DIFFRACTION100
2.2954-35.09050.18431420.16829304X-RAY DIFFRACTION100

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