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- PDB-5fgm: Streptomyces coelicolor SigR region 4 -

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Basic information

Entry
Database: PDB / ID: 5fgm
TitleStreptomyces coelicolor SigR region 4
ComponentsECF RNA polymerase sigma factor SigR
KeywordsHYDROLASE / ECF sigma factors / sigma factor region 4 / promoter -35 element binding
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / response to oxidative stress / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
RNA polymerase sigma-70, actinobacteria / 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, actinobacteria / 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
ECF RNA polymerase sigma factor SigR
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPark, S.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: In Streptomyces coelicolor SigR, methionine at the -35 element interacting region 4 confers the -31'-adenine base selectivity
Authors: Kim, K.Y. / Park, J.K. / Park, S.Y.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECF RNA polymerase sigma factor SigR


Theoretical massNumber of molelcules
Total (without water)7,9911
Polymers7,9911
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4480 Å2
2
A: ECF RNA polymerase sigma factor SigR

A: ECF RNA polymerase sigma factor SigR


Theoretical massNumber of molelcules
Total (without water)15,9812
Polymers15,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1270 Å2
ΔGint-7 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 42.139, 102.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ECF RNA polymerase sigma factor SigR / ECF sigma factor SigR / Alternative RNA polymerase sigma factor SigR / RNA polymerase sigma-R ...ECF sigma factor SigR / Alternative RNA polymerase sigma factor SigR / RNA polymerase sigma-R factor / Sigma-R factor


Mass: 7990.549 Da / Num. of mol.: 1 / Fragment: UNP residues 143-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: sigR, SCO5216 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AKG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 20-30%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 3011 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 55.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 15 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 8.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.95 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.842 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31798 135 4.3 %RANDOM
Rwork0.23879 ---
obs0.2424 3011 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.839 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--1.87 Å20 Å2
3----3.73 Å2
Refinement stepCycle: 1 / Resolution: 2.6→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 0 11 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.978701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50522.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.041595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.714157
X-RAY DIFFRACTIONr_chiral_restr0.1260.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.5321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7362511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6923201
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8164.5190
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.593 6 -
Rwork0.343 220 -
obs--100 %

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