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- PDB-1l5z: CRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1l5z
TitleCRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD
ComponentsC4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
KeywordsTRANSCRIPTION REGULATOR / two component receiver domain / sigma 54 / regulator of AAA+ ATPase
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm
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 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / 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 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
C4-dicarboxylate transport transcriptional regulatory protein DctD
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, S. / Meyer, M. / Jones, A.D. / Yennawar, H.P. / Yennawar, N.H. / Nixon, B.T.
Citation
Journal: FASEB J. / Year: 2002
Title: Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain
Authors: Park, S. / Meyer, M. / Jones, A.D. / Yennawar, H.P. / Yennawar, N.H. / Nixon, B.T.
#1: Journal: FASEB J. / Year: 2001
Title: A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD
Authors: Meyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / McKinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Yennawar, H. / Farber, G.K. / Nixon, B.T.
History
DepositionMar 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2866
Polymers16,8211
Non-polymers4645
Water2,594144
1
A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,57212
Polymers33,6432
Non-polymers92910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
2
A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,14324
Polymers67,2854
Non-polymers1,85820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10020 Å2
ΔGint-35 kcal/mol
Surface area25400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.129, 58.139, 168.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-574-

HOH

31A-578-

HOH

Detailsanalytical ultracentrifuge data indicates solution form is a dimer; genetic and biochemical data indicates substitution destabilizes the dimer ~20-fold, leading to 'derepression' of the ATPase domain asymmetric unit is a monomer biological unit is a dimer - build with symmetry operation -X, -Y, Z

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Components

#1: Protein C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD / DctDNL


Mass: 16821.326 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN, RESIDUES 2-143 / Mutation: E121K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: dctD / Plasmid: pT143E121K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/De3/pLysS / References: UniProt: P13632
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, lithium sulfate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium succinate1reservoirpH5.6
265-75 mM1reservoirHN4H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2001 / Details: MSC Blue Confocal Optical System
RadiationMonochromator: MSC Blue Confocal Optical System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→36.7 Å / Num. all: 19264 / Num. obs: 19264 / % possible obs: 98.6 % / Observed criterion σ(I): 2.2 / Redundancy: 3.04 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3548 / % possible all: 97.5
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 98.9 % / Num. measured all: 59135
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
CNS1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKK

1qkk


Resolution: 2→36.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 215180.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1897 9.8 %RANDOM
Rwork0.196 ---
all-19264 --
obs-19264 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.2093 Å2 / ksol: 0.385197 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---1.1 Å20 Å2
3---1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 29 144 1263
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it42
X-RAY DIFFRACTIONc_scangle_it4.922.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 318 10.1 %
Rwork0.246 2818 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP1.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CRY.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
% reflection Rfree: 9.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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