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- PDB-2o8x: Crystal structure of the "-35 element" promoter recognition domai... -

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Basic information

Entry
Database: PDB / ID: 2o8x
TitleCrystal structure of the "-35 element" promoter recognition domain of Mycobacterium tuberculosis SigC
ComponentsProbable RNA polymerase sigma-C factor
KeywordsTRANSCRIPTION / promoter recognition / transcription regulation / helix-turn-helix motif
Function / homology
Function and homology information


response to water / sigma factor activity / DNA-templated transcription initiation / response to heat / response to hypoxia / response to xenobiotic stimulus / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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 ...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 SigC / ECF RNA polymerase sigma factor SigC
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsThakur, K.G. / Joshi, A.M. / Gopal, B.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis.
Authors: Thakur, K.G. / Joshi, A.M. / Gopal, B.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable RNA polymerase sigma-C factor
B: Probable RNA polymerase sigma-C factor
C: Probable RNA polymerase sigma-C factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,02412
Polymers22,1593
Non-polymers8659
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-164 kcal/mol
Surface area8870 Å2
MethodPISA
2
A: Probable RNA polymerase sigma-C factor
B: Probable RNA polymerase sigma-C factor
C: Probable RNA polymerase sigma-C factor
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)276,284144
Polymers265,90936
Non-polymers10,375108
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area75660 Å2
ΔGint-2123 kcal/mol
Surface area91480 Å2
MethodPISA
3
A: Probable RNA polymerase sigma-C factor
B: Probable RNA polymerase sigma-C factor
C: Probable RNA polymerase sigma-C factor
hetero molecules

A: Probable RNA polymerase sigma-C factor
B: Probable RNA polymerase sigma-C factor
C: Probable RNA polymerase sigma-C factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,04724
Polymers44,3186
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_554-x+1/2,y,-z-1/21
Buried area11150 Å2
ΔGint-345 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.330, 161.330, 161.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Probable RNA polymerase sigma-C factor


Mass: 7386.354 Da / Num. of mol.: 3 / Fragment: Region 4, Promoter -35 element recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: sigC / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: P66809, UniProt: P9WGH1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M ammonium sulphate, 0.1M MES (pH 6.5), 1mM DTT, 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40.29 Å / Num. obs: 7040 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Redundancy: 3.4 % / Rsym value: 0.105 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1002 / Rsym value: 0.546

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OR7

1or7


Resolution: 3→37.01 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.841 / SU B: 16.305 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.744 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27131 331 4.7 %RANDOM
Rwork0.21359 ---
obs0.21628 6707 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.157 Å2
Refinement stepCycle: LAST / Resolution: 3→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 45 17 1408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2352.0271887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.6115180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12722.94151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.48415228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1691515
X-RAY DIFFRACTIONr_chiral_restr0.1640.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02972
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.2778
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.2972
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.217
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_it0.6161.5919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12821437
X-RAY DIFFRACTIONr_scbond_it1.873499
X-RAY DIFFRACTIONr_scangle_it3.2444.5450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 27 -
Rwork0.297 466 -
obs--97.43 %

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