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- PDB-1h3l: N-terminal fragment of SigR from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 1h3l
TitleN-terminal fragment of SigR from Streptomyces coelicolor
ComponentsRNA POLYMERASE SIGMA FACTOR
KeywordsTRANSCRIPTION / DNA-BINDING / TRANSCRIPTION REGULATION
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 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 ...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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ECF RNA polymerase sigma factor SigR / ECF RNA polymerase sigma factor SigR
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.375 Å
AuthorsLi, W. / Stevenson, C.E.M. / Burton, N. / Jakimowicz, P. / Paget, M.S.B. / Buttner, M.J. / Lawson, D.M. / Kleanthous, C.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Identification and Structure of the Anti-Sigma Factor-Binding Domain of the Disulfide-Stress Regulated Sigma Factor Sigma(R) from Streptomyces Coelicolor
Authors: Li, W. / Stevenson, C.E.M. / Burton, N. / Jakimowicz, P. / Paget, M.S.B. / Buttner, M.J. / Lawson, D.M. / Kleanthous, C.
History
DepositionSep 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA POLYMERASE SIGMA FACTOR
B: RNA POLYMERASE SIGMA FACTOR


Theoretical massNumber of molelcules
Total (without water)20,3152
Polymers20,3152
Non-polymers00
Water1267
1
A: RNA POLYMERASE SIGMA FACTOR


Theoretical massNumber of molelcules
Total (without water)10,1571
Polymers10,1571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA POLYMERASE SIGMA FACTOR


Theoretical massNumber of molelcules
Total (without water)10,1571
Polymers10,1571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.546, 71.546, 102.794
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.23955, -0.43961, -0.86566), (-0.42144, 0.75615, -0.50062), (0.87465, 0.48474, -0.00413)
Vector: 48.22181, 47.8491, 3.70409)

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Components

#1: Protein RNA POLYMERASE SIGMA FACTOR / SIGR / SCO5216 / SC7E4.13


Mass: 10157.266 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 23-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria)
Strain: M145 / Plasmid: PET15B-SIGR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O87834, UniProt: Q7AKG9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFRAGMENT PRODUCED BY PROTEOLYSIS OF THE FULL-LENGTH PROTEIN

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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: 3.69 Å3/Da / Density % sol: 66 %
Crystal growpH: 8.5
Details: 10-15%(W/V) PEG 8000 IN 100MM TRIS-HCL PH8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210-15 %(w/v)PEG80001reservoir
3100 mMTris-HCl1reservoirpH8.5
41 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 12713 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9
Reflection
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 83.4 % / Rmerge(I) obs: 0.142

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.375→40 Å / SU B: 6.545 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.27823 618 5 %RANDOM
Rwork0.2584 ---
obs0.25939 12713 99.6 %-
Displacement parametersBiso mean: 34.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.375→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 7 1251
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.029
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.44
X-RAY DIFFRACTIONp_chiral_restr0.204
LS refinement shell
*PLUS
Highest resolution: 2.375 Å / Lowest resolution: 2.436 Å / Rfactor Rfree: 0.346 / Rfactor Rwork: 0.287 / Num. reflection Rwork: 842 / Total num. of bins used: 20

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