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- PDB-7vbs: Structure of the AAA+ ATPase domain of the transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 7vbs
TitleStructure of the AAA+ ATPase domain of the transcriptional regulator GtrR in Burkholderia cenocepacia
ComponentsSigma-54 dependent trancsriptional regulator
KeywordsTRANSCRIPTION / Bacterial enhancer-binding protein / AAA+ ATPase / Quorum sensing / Transcriptional regulator
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Sigma-54-dependent Fis family transcriptional regulator
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsYan, X.F. / Yong, Y. / Gao, Y.G.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2019-T2-2-099 Singapore
Ministry of Education (MoE, Singapore)RG108/20 Singapore
CitationJournal: Febs Lett. / Year: 2022
Title: Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum-sensing system in Burkholderia cenocepacia.
Authors: Yan, X.F. / Yang, C. / Wang, M. / Yong, Y. / Deng, Y. / Gao, Y.G.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma-54 dependent trancsriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8432
Polymers51,7481
Non-polymers951
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-8 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.678, 108.678, 40.375
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Sigma-54 dependent trancsriptional regulator / Sigma-54-dependent Fis family transcriptional regulator


Mass: 51747.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: ntrC_2, A3203_18285, A8E72_13470, NCTC13227_05325 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V2W4X9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.34 Å3/Da / Density % sol: 7.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11% (w/v) Polyethylene glycol 6000, 100 mM Tris-HCl pH 8.1, 100 mM Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.998→37.105 Å / Num. obs: 18704 / % possible obs: 99.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 41.27 Å2 / CC1/2: 1 / Net I/σ(I): 18.33
Reflection shellResolution: 1.998→2.07 Å / Num. unique obs: 1818 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5exs

5exs


Resolution: 1.998→37.105 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 2037 10.9 %
Rwork0.1982 16650 -
obs0.2004 18687 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.7 Å2 / Biso mean: 55.6864 Å2 / Biso min: 28.57 Å2
Refinement stepCycle: final / Resolution: 1.998→37.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 5 149 2011
Biso mean--46.41 60.82 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031919
X-RAY DIFFRACTIONf_angle_d0.6752599
X-RAY DIFFRACTIONf_chiral_restr0.023291
X-RAY DIFFRACTIONf_plane_restr0.005337
X-RAY DIFFRACTIONf_dihedral_angle_d13.214695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9981-2.04460.37021380.3665105497
2.0446-2.09570.39251260.33151103100
2.0957-2.15240.32361080.3041137100
2.1524-2.21570.3091070.3061146100
2.2157-2.28720.39841440.33631071100
2.2872-2.36890.31081390.25161122100
2.3689-2.46380.29181340.23681099100
2.4638-2.57590.28111490.2321093100
2.5759-2.71160.21351380.22251101100
2.7116-2.88150.2571320.2281111100
2.8815-3.10390.26731360.22181113100
3.1039-3.4160.22651380.20881119100
3.416-3.90980.16921540.1721087100
3.9098-4.92420.1621390.13491132100
4.9242-37.1050.17381550.16451162100
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)
15.9191-0.06512.11434.419-0.06825.37610.12770.0702-1.226-0.088-0.01320.1930.8622-0.0332-0.11140.3721-0.01020.0170.2645-0.02490.4558-8.0075-40.36932.6682
26.04151.26820.85377.3814-0.44493.077-0.01620.39790.4304-0.80930.1388-0.0913-0.2177-0.2408-0.02510.38890.03040.06220.37490.01720.3119-8.2795-22.4837-7.684
34.8975-0.71291.49985.63880.11344.760.06890.3250.0818-0.48810.00930.0914-0.3633-0.1056-0.07790.2597-0.018-0.01730.2856-0.00730.2402-13.9735-20.5362-2.1355
46.4756-4.3368-0.68835.59160.25821.0493-0.5115-0.7773-0.35970.76970.45130.06140.00590.06490.04690.37160.00870.02140.36260.02810.2524-10.6259-29.55912.2739
56.66510.0176-3.45587.3521.80066.6729-0.17291.0666-0.94920.2252-0.2670.9370.4564-1.23040.22750.46410.0533-0.10460.3993-0.05950.640811.4157-46.9173.165
65.44190.0713.74358.9155-1.15927.83160.22720.1942-1.0445-1.15990.30850.33460.4009-0.9827-0.21250.82980.12210.12530.43350.12920.536221.0868-52.7802-3.2941
74.5996-2.014-1.07323.93941.31162.1451-0.74-1.8112-1.09040.74670.78480.1540.32070.4727-0.0730.49460.14030.06090.48130.15810.453615.5311-44.675213.2041
85.8728-6.0749-6.59368.23576.2828.04270.3501-0.610.4592-0.49440.2463-0.4327-0.10760.318-0.27690.40650.034-0.06240.25560.06110.421717.0838-39.20721.5927
93.8789-1.07790.52866.88995.61936.870.07360.14960.3436-0.7026-0.205-0.4022-0.63150.8390.28870.47490.0321-0.07390.43180.08210.585226.6813-42.72615.9872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 139 through 180 )A139 - 180
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 231 )A181 - 231
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 277 )A232 - 277
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 312 )A278 - 312
5X-RAY DIFFRACTION5chain 'A' and (resid 313 through 328 )A313 - 328
6X-RAY DIFFRACTION6chain 'A' and (resid 329 through 340 )A329 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 354 )A341 - 354
8X-RAY DIFFRACTION8chain 'A' and (resid 355 through 373 )A355 - 373
9X-RAY DIFFRACTION9chain 'A' and (resid 374 through 385 )A374 - 385

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