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- PDB-6ido: Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusin... -

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Basic information

Entry
Database: PDB / ID: 6ido
TitleCrystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA
Components
  • DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')
  • DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')
  • RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix
KeywordsTRANSCRIPTION / sigma4 / sigmaS / -35 element DNA
Function / homology
Function and homology information


DNA-templated transcription initiation => GO:0006352 / bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / 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 factor RpoS / Sigma-70 factors family signature 1. / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor RpoS / RNA polymerase sigma factor RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Klebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.748 Å
AuthorsLou, Y.C. / Chien, C.Y. / Chen, C. / Hsu, C.H.
CitationJournal: Proteins / Year: 2020
Title: Structural basis for -35 element recognition by sigma4chimera proteins and their interactions with PmrA response regulator.
Authors: Lou, Y.C. / Chou, C.C. / Yeh, H.H. / Chien, C.Y. / Sadotra, S. / Hsu, C.H. / Chen, C.
History
DepositionSep 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix
C: DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')
B: RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix
E: DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')
F: DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)44,9086
Polymers44,9086
Non-polymers00
Water0
1
A: RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix
C: DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)22,4543
Polymers22,4543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-17 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix
E: DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')
F: DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)22,4543
Polymers22,4543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-15 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.540, 154.540, 144.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix / Sigma S


Mass: 12946.672 Da / Num. of mol.: 2 / Mutation: T79G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: rpoS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9F8R5, UniProt: P13445*PLUS
#2: DNA chain DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')


Mass: 4640.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
#3: DNA chain DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')


Mass: 4867.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)

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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: 4.9 Å3/Da / Density % sol: 74.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate (pH 4.6), and 25% w/v Polyethylene glycol 4,000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.748→29.616 Å / Num. obs: 13130 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 42.909
Reflection shellResolution: 3.748→3.88 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4.333 / Num. unique obs: 871 / Rsym value: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IPL

5ipl


Resolution: 3.748→29.616 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2525 1314 10.01 %
Rwork0.2226 --
obs0.2256 13125 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.748→29.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 1230 0 0 2570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042726
X-RAY DIFFRACTIONf_angle_d0.6763919
X-RAY DIFFRACTIONf_dihedral_angle_d20.8921423
X-RAY DIFFRACTIONf_chiral_restr0.036447
X-RAY DIFFRACTIONf_plane_restr0.003292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7481-3.89790.26371070.2733871X-RAY DIFFRACTION52
3.8979-4.07490.3246940.2472923X-RAY DIFFRACTION53
4.0749-4.28910.30211080.259897X-RAY DIFFRACTION53
4.2891-4.55690.3151960.237938X-RAY DIFFRACTION53
4.5569-4.90730.24941480.22851307X-RAY DIFFRACTION77
4.9073-5.39850.26461860.21521715X-RAY DIFFRACTION100
5.3985-6.17350.24481870.21181727X-RAY DIFFRACTION100
6.1735-7.75480.19841940.20781719X-RAY DIFFRACTION100
7.7548-29.61690.22791940.20081714X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01410.01640.00090.0391-0.01330.0112-0.0148-0.03640.06430.11730.0876-0.0478-0.0277-0.0668-0.00180.20430.26480.07110.24840.32410.387630.1722-15.0215-22.0917
20.00280.0124-0.00280.02390.01250.00620.00910.04340.03680.09770.00890.0183-0.0286-0.1497-0.00080.0930.05770.55320.65490.36460.225721.9198-17.6081-28.6515
30.00370.00590.01070.00270.00490.0485-0.09950.0366-0.02010.0682-0.1466-0.0465-0.16560.0417-0.03120.49850.12610.14710.18840.15820.668930.8703-2.2725-24.1614
40.00230.0278-0.00120.0188-0.01790.02690.16210.15040.0471-0.08640.08910.13910.1246-0.12260.194-0.44450.24930.60860.82250.1587-0.051816.5879-21.6914-40.6998
50.17420.07480.04150.1323-0.03350.01680.2115-0.04710.1757-0.0857-0.1917-0.03920.1576-0.38890.006-0.22040.04550.46180.97430.2140.354319.0569-18.9357-41.0461
60.00440.00090.00080.0039-0.00120.0011-0.0483-0.01920.02010.0036-0.005-0.03080.007-0.1349-0.00010.75210.06460.32680.77080.14350.548730.8902-17.6003-9.6762
70.01480.03170.00780.07050.01770.00630.03490.04910.00950.05160.02480.01390.0269-0.00640.04670.42580.24440.1126-0.03960.02850.107342.5136-17.9683-13.2463
80.001-0.00420.00050.0485-0.0480.05360.08490.01440.04340.03470.1285-0.12090.014-0.03690.09420.48840.22840.10270.2108-0.05550.382547.906-20.6325-17.9569
90.0591-0.08550.10370.1502-0.16340.1980.0933-0.14850.0940.19520.25940.01570.0406-0.14980.30440.72780.25740.11240.0882-0.27520.194840.6968-23.1932-5.6553
100.01780.0576-0.06840.0879-0.08950.15430.1951-0.04630.08210.23240.072-0.2211-0.06840.24330.23220.6770.2113-0.4296-0.0454-0.93160.273460.5682-20.4592-7.1398
110.15940.1593-0.10740.2514-0.02370.16320.2785-0.15250.2260.03850.1258-0.25140.0340.20570.39610.67910.3226-0.27480.1453-0.79790.381758.7171-23.4228-6.9873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 111 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 15 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 38 )
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 111 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 15 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 15 )

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