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- PDB-1or7: Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic... -

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Basic information

Entry
Database: PDB / ID: 1or7
TitleCrystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA
Components
  • RNA polymerase sigma-E factor
  • Sigma-E factor negative regulatory protein
KeywordsTRANSCRIPTION / regulation / DNA-BINDING / TRANSMEMBRANE
Function / homology
Function and homology information


sigma factor antagonist activity / 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 ...sigma factor antagonist activity / 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 / molecular adaptor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
Anti sigma-E protein RseA, N-terminal domain / Sigma-E factor negative regulatory protein RseA / Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain / RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 ...Anti sigma-E protein RseA, N-terminal domain / Sigma-E factor negative regulatory protein RseA / Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal 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/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
Anti-sigma-E factor RseA / ECF RNA polymerase sigma-E factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCampbell, E.A. / Tupy, J.L. / Gruber, T.M. / Wang, S. / Sharp, M.M. / Gross, C.A. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA.
Authors: Campbell, E.A. / Tupy, J.L. / Gruber, T.M. / Wang, S. / Sharp, M.M. / Gross, C.A. / Darst, S.A.
History
DepositionMar 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma-E factor
C: Sigma-E factor negative regulatory protein
B: RNA polymerase sigma-E factor
F: Sigma-E factor negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)64,8254
Polymers64,8254
Non-polymers00
Water3,153175
1
A: RNA polymerase sigma-E factor
C: Sigma-E factor negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)32,4132
Polymers32,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-27 kcal/mol
Surface area12650 Å2
MethodPISA
2
B: RNA polymerase sigma-E factor
F: Sigma-E factor negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)32,4132
Polymers32,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-31 kcal/mol
Surface area10910 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-74 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.049, 56.901, 104.981
Angle α, β, γ (deg.)90.00, 130.51, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a heterodimer of sigma E (chains A,B) plus RseA (chain C), or chains (D,E) plus chain F

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Components

#1: Protein RNA polymerase sigma-E factor / Sigma-24


Mass: 22003.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: RPOE OR SIGE OR B2573 OR C3097 OR Z3855 OR ECS3439 OR SF2635
Plasmid: pLC31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AGB6
#2: Protein Sigma-E factor negative regulatory protein


Mass: 10408.719 Da / Num. of mol.: 2 / Fragment: RseA-N, residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RSEA OR MCLA OR B2572 OR C3096 / Plasmid: pLC31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AFX7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.82 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium formate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
21.6 Msodium formate1reservoir
30.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 84266 / Num. obs: 82833 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.083 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4296 / Rsym value: 0.359 / % possible all: 92.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 35 Å / Num. measured all: 181227 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.101 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.162 / ESU R Free: 0.148
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23149 2134 5 %RANDOM
Rwork0.19705 ---
all0.1987 ---
obs0.19879 40441 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.358 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å21.1 Å2
2---0.27 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 0 175 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213873
X-RAY DIFFRACTIONr_bond_other_d0.0010.023579
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9595228
X-RAY DIFFRACTIONr_angle_other_deg1.12538280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1593470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49815715
X-RAY DIFFRACTIONr_chiral_restr0.080.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024294
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02799
X-RAY DIFFRACTIONr_nbd_refined0.2570.31060
X-RAY DIFFRACTIONr_nbd_other0.2270.33618
X-RAY DIFFRACTIONr_nbtor_other0.3350.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5204
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3310.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.519
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0090.51
X-RAY DIFFRACTIONr_mcbond_it0.8451.52370
X-RAY DIFFRACTIONr_mcangle_it1.62223821
X-RAY DIFFRACTIONr_scbond_it2.88431503
X-RAY DIFFRACTIONr_scangle_it4.7664.51407
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 165
Rwork0.3 2975
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6713-1.9986-1.34332.79220.29481.7385-0.2552-0.3705-0.6902-0.04460.15150.35040.18270.01130.10370.11840.0197-0.00060.21670.09390.1799-2.930248.401824.8395
23.1163-1.3176-0.90015.29031.51683.48850.0856-0.26740.3696-0.2693-0.0258-0.5106-0.25710.2772-0.05980.1105-0.0481-0.02580.2411-0.03860.21315.336974.006928.83
32.2551-0.6138-0.04423.06821.00772.75380.05520.00850.1336-0.4436-0.20860.1297-0.1044-0.15550.15340.14650.0341-0.0270.2206-0.01020.1047-5.175665.05421.2894
43.1951-1.1555-0.42753.4311-0.0172.3147-0.1648-0.3888-0.24940.24480.23920.21840.1008-0.1417-0.07440.09670.03980.01580.09420.04490.051427.665135.412120.1517
51.89940.177-0.38093.3287-0.74351.88780.0317-0.0520.0792-0.14970.07240.2331-0.1142-0.1311-0.1040.0536-0.0043-0.03690.01070.02270.063128.582549.6457-0.6756
62.1122-0.5267-0.20142.0264-0.18821.6793-0.0289-0.22280.21790.24910.0762-0.1793-0.06530.1705-0.04720.11080.0127-0.0270.0714-0.02130.104335.0445.509712.0299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1115 - 114
2X-RAY DIFFRACTION2AA123 - 187126 - 190
3X-RAY DIFFRACTION3CB1 - 664 - 66
4X-RAY DIFFRACTION4BC2 - 915 - 94
5X-RAY DIFFRACTION5BC122 - 190125 - 192
6X-RAY DIFFRACTION6FD1 - 641 - 64
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48

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