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- PDB-6dxo: 1.8 A structure of RsbN-BldN complex. -

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Basic information

Entry
Database: PDB / ID: 6dxo
Title1.8 A structure of RsbN-BldN complex.
Components
  • BldN
  • RNA polymerase ECF-subfamily sigma factor
KeywordsTRANSCRIPTION / BldN / RsbN / Sigma / anti-sigma / ECF
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / membrane => GO:0016020 / DNA binding
Similarity search - Function
RNA polymerase sigma-X type / Domain of unknown function DUF5667 / Domain of unknown function (DUF5667) / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / 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-X type / Domain of unknown function DUF5667 / Domain of unknown function (DUF5667) / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / 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
Similarity search - Domain/homology
Putative RNA polymerase ECF-subfamily sigma factor / DUF5667 domain-containing protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The crystal structure of the RsbN-sigma BldN complex from Streptomyces venezuelae defines a new structural class of anti-sigma factor.
Authors: Schumacher, M.A. / Bush, M.J. / Bibb, M.J. / Ramos-Leon, F. / Chandra, G. / Zeng, W. / Buttner, M.J.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 11, 2018ID: 6C03
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase ECF-subfamily sigma factor
D: BldN


Theoretical massNumber of molelcules
Total (without water)26,6122
Polymers26,6122
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-20 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.409, 43.375, 58.715
Angle α, β, γ (deg.)90.000, 111.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA polymerase ECF-subfamily sigma factor


Mass: 17165.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_3185 / Production host: Escherichia coli / References: UniProt: F2R911*PLUS
#2: Protein BldN


Mass: 9446.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_3186 / Production host: Escherichia coli / References: UniProt: F2R912
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium nitrate, 26% PEG 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.8→23.06 Å / Num. obs: 29209 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.044 / Rrim(I) all: 0.075 / Rsym value: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.9 / CC1/2: 0.977 / Rpim(I) all: 0.101 / Rrim(I) all: 0.17 / Rsym value: 0.136 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C03

6c03
PDB Unreleased entry


Resolution: 1.8→23.06 Å / FOM work R set: 0.82 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 2626 8.99 %
Rwork0.2028 26583 -
obs0.206 29209 77.49 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.058 Å2 / ksol: 0.453 e/Å3
Displacement parametersBiso max: 143.16 Å2 / Biso mean: 38.4 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--6.8162 Å20 Å2-5.9694 Å2
2---4.0778 Å2-0 Å2
3---10.894 Å2
Refinement stepCycle: final / Resolution: 1.8→23.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 135 1681
Biso mean---46.91 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071566
X-RAY DIFFRACTIONf_angle_d0.8982114
X-RAY DIFFRACTIONf_chiral_restr0.061243
X-RAY DIFFRACTIONf_plane_restr0.004275
X-RAY DIFFRACTIONf_dihedral_angle_d13.424576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86430.32462580.27322777303580
1.8643-1.93890.282640.23772770303480
1.9389-2.02710.2312750.20972759303481
2.0271-2.13390.24662680.20422768303681
2.1339-2.26750.24162740.19692769304381
2.2675-2.44240.24572810.19872780306181
2.4424-2.68790.25332740.19882780305481
2.6879-3.0760.23522800.19312717299780
3.076-3.87250.21412680.17912618288676
3.8725-23.06170.22711840.22571845202954
Refinement TLS params.Method: refined / Origin x: -5.5551 Å / Origin y: 0.569 Å / Origin z: 24.9492 Å
111213212223313233
T0.1343 Å2-0.0002 Å2-0.005 Å2-0.107 Å20.0314 Å2--0.1232 Å2
L1.3907 °20.8989 °2-0.0433 °2-1.1169 °20.9491 °2--0.8459 °2
S-0.0142 Å °0.0441 Å °-0.0897 Å °-0.079 Å °0.1143 Å °-0.1357 Å °-0.0194 Å °0.0692 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 172
2X-RAY DIFFRACTION1allD2 - 79
3X-RAY DIFFRACTION1allS1 - 137

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