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- PDB-2p7v: Crystal structure of the Escherichia coli regulator of sigma 70, ... -

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Basic information

Entry
Database: PDB / ID: 2p7v
TitleCrystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4
Components
  • RNA polymerase sigma factor rpoD
  • Regulator of sigma D
KeywordsTRANSCRIPTION / Rsd / sigma 70 / Regulator of sigma 70 / sigma 70 domain 4 / regulation / Helix-turn-helix / Rsd-sigma 70 complex / sigma factor / Escherichia coli Rsd-sigma 70 complex / E. coli Rsd-sigma 70 complex
Function / homology
Function and homology information


positive regulation of nucleotide catabolic process / sigma factor antagonist activity / bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat ...positive regulation of nucleotide catabolic process / sigma factor antagonist activity / bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Regulator of RNA polymerase sigma(70) subunit, domain 4 / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Regulator of RNA polymerase sigma(70) subunit, Rsd / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ superfamily / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 ...Regulator of RNA polymerase sigma(70) subunit, domain 4 / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / Regulator of RNA polymerase sigma(70) subunit, Rsd / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ superfamily / Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD / Regulator of sigma D / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsPatikoglou, G.A. / Westblade, L.F. / Campbell, E.A. / Lamour, V. / Lane, W.J. / Darst, S.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.
Authors: Patikoglou, G.A. / Westblade, L.F. / Campbell, E.A. / Lamour, V. / Lane, W.J. / Darst, S.A.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Regulator of sigma D
B: RNA polymerase sigma factor rpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2683
Polymers26,2442
Non-polymers241
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Regulator of sigma D
B: RNA polymerase sigma factor rpoD
hetero molecules

A: Regulator of sigma D
B: RNA polymerase sigma factor rpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5376
Polymers52,4884
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area6610 Å2
ΔGint-32 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.111, 84.111, 84.219
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-101-

MG

21A-169-

HOH

DetailsThe biological assembly consists of one Rsd - sigma 70 domain 4 protein-protein complex.

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Components

#1: Protein Regulator of sigma D


Mass: 18266.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsd / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFX4
#2: Protein RNA polymerase sigma factor rpoD / Sigma-70


Mass: 7977.170 Da / Num. of mol.: 1 / Fragment: domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoD, alt / Production host: Escherichia coli (E. coli) / References: UniProt: P00579, UniProt: Q0P6L9*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M KCl, 0.05 M MgCl2, 0.05 M Tris-HCl, pH 7.5, and 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONAPS 31-ID20.9793, 0.9641
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97931
30.96411
ReflectionResolution: 2.6→50 Å / Num. all: 10405 / Num. obs: 10405 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 513 4.9 %Random
Rwork0.239 ---
all0.24 10405 --
obs0.24 10405 99.1 %-
Solvent computationBsol: 29.183 Å2
Displacement parametersBiso mean: 42.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.158 Å2-8.887 Å20 Å2
2--0.158 Å20 Å2
3----0.315 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 1 94 1865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.328
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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