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- PDB-4ki2: Crystallographic analysis of an RNA-polymerase sigma-subunit frag... -

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Basic information

Entry
Database: PDB / ID: 4ki2
TitleCrystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA
Components
  • DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
  • RNA polymerase sigma factor
KeywordsTranscription/DNA / ssDNA / G-quartet / G-quadruplex / promoter recognition / promoter opening / transcription initiation / protein-DNA binding / ssDNA-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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal 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: 3.3 Å
AuthorsFeklistov, A. / Darst, S.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes.
Authors: Feklistov, A. / Darst, S.A.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionSep 4, 2013ID: 4GOR
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
D: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
E: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
F: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
G: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
A: RNA polymerase sigma factor
B: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92511
Polymers69,7306
Non-polymers1955
Water00
1
D: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
G: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0608
Polymers34,8653
Non-polymers1955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
F: DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
B: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)34,8653
Polymers34,8653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.110, 118.110, 200.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11D-101-

K

21D-102-

K

31D-103-

K

41G-101-

K

51G-102-

K

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Components

#1: DNA chain
DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')


Mass: 3413.246 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: sequence from non-template strand of -10 bacterial promoter element
#2: Protein RNA polymerase sigma factor


Mass: 28038.398 Da / Num. of mol.: 2 / Fragment: domains 2-3, (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
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 5% w/v PEG8000, 20% w/v PEG300, 10% v/v glycerol, 0.15% w/v mellitic acid, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2009
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→29.53 Å / Num. all: 13096 / Num. obs: 13060 / % possible obs: 99.98 % / Redundancy: 14.4 %
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 620 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→29.53 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1306 10 %
Rwork0.2116 --
obs0.2163 13056 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 569 5 0 3726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013925
X-RAY DIFFRACTIONf_angle_d1.3765424
X-RAY DIFFRACTIONf_dihedral_angle_d20.4231527
X-RAY DIFFRACTIONf_chiral_restr0.072591
X-RAY DIFFRACTIONf_plane_restr0.005616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.43160.41771400.37081263X-RAY DIFFRACTION100
3.4316-3.58750.36621420.32761277X-RAY DIFFRACTION100
3.5875-3.77630.30781410.271263X-RAY DIFFRACTION100
3.7763-4.01230.26261420.22671277X-RAY DIFFRACTION100
4.0123-4.32130.22391430.17981288X-RAY DIFFRACTION100
4.3213-4.75450.24521440.17641302X-RAY DIFFRACTION100
4.7545-5.43880.21431460.17951306X-RAY DIFFRACTION100
5.4388-6.83820.25541480.22591336X-RAY DIFFRACTION100
6.8382-29.530.25991600.19051438X-RAY DIFFRACTION100

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