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- PDB-3ugo: Crystal structure of RNA-polymerase sigma subunit domain 2 comple... -

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Basic information

Entry
Database: PDB / ID: 3ugo
TitleCrystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TACAAT)
Components
  • 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / bacterial promoter opening / G-quartet / G-quadruplex / DNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / 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 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsFeklistov, A. / Darst, S.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.
Authors: Feklistov, A. / Darst, S.A.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _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: RNA polymerase sigma factor
B: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
C: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0608
Polymers34,8653
Non-polymers1955
Water2,360131
1
A: RNA polymerase sigma factor
B: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5695
Polymers31,4522
Non-polymers1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-2 kcal/mol
Surface area11580 Å2
MethodPISA
2
C: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules

C: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules

C: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules

C: 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,96612
Polymers13,6534
Non-polymers3138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area1160 Å2
ΔGint-11 kcal/mol
Surface area3930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.134, 86.134, 111.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11B-12-

K

21B-13-

K

31B-14-

K

41C-12-

K

51C-13-

K

61B-107-

HOH

71B-108-

HOH

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Components

#1: Protein RNA polymerase sigma factor


Mass: 28038.398 Da / Num. of mol.: 1 / Fragment: domain 2 (UNP residues 92-332)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EZJ8
#2: DNA chain 5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'


Mass: 3413.246 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG8000, 20% PEG300, 10% glycerol, 0.15% mellitic acid, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.096→25 Å / Num. all: 25331 / Num. obs: 25306 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 33.55
Reflection shellResolution: 2.096→2.18 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 4.04 / Num. unique all: 2471 / Rsym value: 0.712 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KU2

1ku2


Resolution: 2.096→24.483 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 1318 5.21 %
Rwork0.1961 --
obs0.1982 25306 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.4827 Å2-0 Å20 Å2
2---11.4827 Å2-0 Å2
3---23.1439 Å2
Refinement stepCycle: LAST / Resolution: 2.096→24.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 313 5 131 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081874
X-RAY DIFFRACTIONf_angle_d1.1212594
X-RAY DIFFRACTIONf_dihedral_angle_d19.478759
X-RAY DIFFRACTIONf_chiral_restr0.056287
X-RAY DIFFRACTIONf_plane_restr0.003281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.096-2.18030.31691690.28152574X-RAY DIFFRACTION100
2.1803-2.27950.25051510.2322603X-RAY DIFFRACTION100
2.2795-2.39960.24511360.20222636X-RAY DIFFRACTION100
2.3996-2.54980.21951390.19992629X-RAY DIFFRACTION100
2.5498-2.74640.25481380.19912644X-RAY DIFFRACTION100
2.7464-3.02230.24951630.21352625X-RAY DIFFRACTION100
3.0223-3.45860.22851350.19592682X-RAY DIFFRACTION100
3.4586-4.35350.20461460.16682715X-RAY DIFFRACTION100
4.3535-24.48450.23811410.192880X-RAY DIFFRACTION100

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