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- PDB-2h27: Crystal Structure of Escherichia coli SigmaE Region 4 Bound to it... -

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Basic information

Entry
Database: PDB / ID: 2h27
TitleCrystal Structure of Escherichia coli SigmaE Region 4 Bound to its-35 Element DNA
Components
  • 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'
  • 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3'
  • RNA polymerase Sigma E factor
Keywordstransferase/DNA / Protein-DNA Complex / Helix-Turn-Helix / Double Helix / transferase-DNA COMPLEX
Function / homology
Function and homology information


sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription ...sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
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-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 ...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-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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / ECF RNA polymerase sigma-E factor
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLane, W.J. / Darst, S.A.
CitationJournal: Plos Biol. / Year: 2006
Title: The structural basis for promoter -35 element recognition by the group IV sigma factors.
Authors: Lane, W.J. / Darst, S.A.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3'
C: 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'
E: 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3'
F: 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'
A: RNA polymerase Sigma E factor
D: RNA polymerase Sigma E factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5697
Polymers31,4516
Non-polymers1181
Water2,450136
1
B: 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3'
C: 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'
A: RNA polymerase Sigma E factor


Theoretical massNumber of molelcules
Total (without water)15,7263
Polymers15,7263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3'
F: 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'
D: RNA polymerase Sigma E factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8444
Polymers15,7263
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.009, 68.709, 61.133
Angle α, β, γ (deg.)90.00, 101.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two biological units. Each biological unit contains one protein part consisting of SigmaE Region 4 and one DNA part consisting of double-stranded DNA.

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Components

#1: DNA chain 5'-D(*CP*CP*CP*GP*GP*AP*AP*CP*TP*TP*CP*G)-3' / Sigma-24


Mass: 3623.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: HPLC Purified
#2: DNA chain 5'-D(*C*CP*GP*AP*AP*GP*TP*TP*CP*CP*GP*G)-3'


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: HPLC Purified
#3: Protein RNA polymerase Sigma E factor


Mass: 8438.787 Da / Num. of mol.: 2 / Fragment: Region 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: rpoE / Plasmid: pWJL3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0AGB6
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% v/v MPD, 0.04M magnesium chloride, 0.05M sodium-cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium chloride11
3sodium-cacodylate11
4H2O11
5MPD12
6magnesium chloride12
7sodium-cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.00004
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 19011 / % possible obs: 97.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 96.1

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Phasing

Phasing MRRfactor: 0.576 / Cor.coef. Fo:Fc: 0.487
Highest resolutionLowest resolution
Rotation3 Å19.99 Å
Translation3 Å19.99 Å
Phasing dm shellResolution: 2.3→20 Å / Delta phi final: 0.205 / FOM : 0.224 / Reflection: 18308

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1801 9 %RANDOM
Rwork0.241 ---
obs0.241 18308 91.8 %-
all-19943 --
Solvent computationBsol: 37.75 Å2
Displacement parametersBiso mean: 38.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å20 Å27.154 Å2
2---8.411 Å20 Å2
3---11.681 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 928 0 144 2202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3582 206
Rwork0.3306 1832
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5CNS_TOPPAR:MPD.PAR

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