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- PDB-4lrx: Crystal Structure of the E.coli DhaR(N)-DhaK complex -

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Basic information

Entry
Database: PDB / ID: 4lrx
TitleCrystal Structure of the E.coli DhaR(N)-DhaK complex
Components
  • PTS-dependent dihydroxyacetone kinase operon regulatory protein
  • PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
KeywordsTransferase/Transcription Regulator / coiled-coil / helix rotation / PAS / GAF / transcription regulation complex / Transferase-Transcription Regulator complex
Function / homology
Function and homology information


monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / transferase complex / glycerol metabolic process / carbohydrate phosphorylation / glycerol catabolic process ...monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / transferase complex / glycerol metabolic process / carbohydrate phosphorylation / glycerol catabolic process / pyruvate metabolic process / sequence-specific DNA binding / DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Dihydroxyacetone kinase DhaK, subunit 1 / Dihydroxyacetone kinase; domain 2 / DhaK domain / Dak1 domain / DhaK domain profile. / Dihydroxyacetone kinase; domain 1 / Hypothetical Protein Tm841; Chain: A;domain 3 / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. ...Dihydroxyacetone kinase DhaK, subunit 1 / Dihydroxyacetone kinase; domain 2 / DhaK domain / Dak1 domain / DhaK domain profile. / Dihydroxyacetone kinase; domain 1 / Hypothetical Protein Tm841; Chain: A;domain 3 / Sigma-54 interaction domain ATP-binding region A 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 / GAF domain / PAS domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS domain / PAS domain superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK / PTS-dependent dihydroxyacetone kinase operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsShi, R. / McDonald, L. / Cygler, M. / Ekiel, I.
CitationJournal: Structure / Year: 2014
Title: Coiled-Coil Helix Rotation Selects Repressing or Activating State of Transcriptional Regulator DhaR.
Authors: Shi, R. / McDonald, L. / Cygler, M. / Ekiel, I.
History
DepositionJul 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
B: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
C: PTS-dependent dihydroxyacetone kinase operon regulatory protein
D: PTS-dependent dihydroxyacetone kinase operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4666
Polymers146,2824
Non-polymers1842
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-71 kcal/mol
Surface area49060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.129, 232.129, 79.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is the same as asym.

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Components

#1: Protein PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK


Mass: 38251.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1200, dhaK, dhaR, JW5187, ycgT / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76015, Transferases; Transferring phosphorus-containing groups
#2: Protein PTS-dependent dihydroxyacetone kinase operon regulatory protein


Mass: 34889.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1201, dhaK, dhaR, JW5188, ycgU / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76016
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 4.25 Å3/Da / Density % sol: 71.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG 200, pH 6.5, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 39071 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.134 / Χ2: 1.016 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.25-3.375.70.52538830.983199.1
3.37-3.56.20.43738350.966199.6
3.5-3.666.60.3438741.01199.3
3.66-3.857.10.25938531.041199.9
3.85-4.097.40.18239061.001199.9
4.09-4.417.80.13538971.009199.9
4.41-4.858.40.11539031.0531100
4.85-5.569.30.12239281.1111100
5.56-79.50.1139461.0421100
7-508.80.04340460.907199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2051 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8718 / SU B: 36.999 / SU ML: 0.27 / SU R Cruickshank DPI: 0.402 / SU Rfree: 0.3891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1958 5 %RANDOM
Rwork0.1913 ---
obs0.193 39037 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 130.31 Å2 / Biso mean: 68.4377 Å2 / Biso min: 38.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å2-1.98 Å20 Å2
2---3.96 Å20 Å2
3---5.95 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9900 0 12 0 9912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210092
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.96213728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68351298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26825.069434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.069151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4241550
X-RAY DIFFRACTIONr_chiral_restr0.1060.21604
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217588
X-RAY DIFFRACTIONr_mcbond_it0.5081.56454
X-RAY DIFFRACTIONr_mcangle_it1.039210354
X-RAY DIFFRACTIONr_scbond_it1.54533638
X-RAY DIFFRACTIONr_scangle_it2.7374.53374
LS refinement shellResolution: 3.246→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 137 -
Rwork0.268 2676 -
all-2813 -
obs--97.3 %
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)
11.3956-0.1291-1.10091.316-0.3983.89160.1621-0.0374-0.0778-0.10150.0097-0.05-0.39120.304-0.17180.1363-0.03930.11210.0319-0.05420.3116.262765.852911.4489
21.67670.3445-0.30671.09680.30534.28410.12960.1309-0.17050.08030.02220.0359-0.3896-0.3762-0.15180.16250.0730.1010.05110.0080.2531-10.50568.725629.5266
32.15772.1841-0.64512.4191-0.89121.2530.0250.0582-0.16710.018-0.0381-0.069-0.52720.15540.01310.3906-0.03570.04290.0596-0.05410.229933.074664.9026-25.245
40.69791.420.39594.87551.39241.164-0.0006-0.0685-0.10260.0081-0.12060.1449-0.41410.19840.12120.2402-0.1118-0.02080.1518-0.01630.161442.654758.1585-28.8414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 356
2X-RAY DIFFRACTION2B1 - 356
3X-RAY DIFFRACTION3C12 - 306
4X-RAY DIFFRACTION4D12 - 306

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