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- PDB-1l5y: CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHI... -

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Basic information

Entry
Database: PDB / ID: 1l5y
TitleCRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD
ComponentsC4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
KeywordsTRANSCRIPTION REGULATOR / Beryllofluoride bound two component receiver domain
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 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / BERYLLIUM DIFLUORIDE / BERYLLIUM TETRAFLUORIDE ION / C4-dicarboxylate transport transcriptional regulatory protein DctD
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). IN THIS ENTRY CHAIN A AND B FORM THE DIMER THAT IS MOST LIKELY TO BE BIOLOGICALLY RELEVANT, BASED ON ITS USE OF THE SIGNALING SURFACE AS A DIMER INTERFACE AND UPON STRONG SIMILARITY TO FIXJ. HOWEVER, OTHER DIMER FORMS ARE PRESENT IN THE CRYSTAL LATTICE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,92123
Polymers33,6432
Non-polymers1,27821
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.005, 76.837, 77.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsanalytical ultracentrifugation indicates solution form is dimeric but which possible dimer or dimers of the crystal lattice are relevant to solution is not yet known

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 16821.326 Da / Num. of mol.: 2 / 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

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Non-polymers , 7 types, 245 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-BF2 / BERYLLIUM DIFLUORIDE / Beryllium fluoride


Mass: 47.009 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: BeF2
#6: Chemical ChemComp-BF4 / BERYLLIUM TETRAFLUORIDE ION / Tetrafluoroberyllate


Mass: 85.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, lithium sulfate, HEPES, beryllium chloride, sodium fluoride, magnesium chloride, pH 7.0, 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 25, 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: 2.1→43.24 Å / Num. all: 18672 / Num. obs: 18672 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.74 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 4.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2 / Num. unique all: 3331 / % possible all: 94.9
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.3 % / Num. measured all: 69850
Reflection shell
*PLUS
% possible obs: 99.3 %

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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: 2.1→19.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 259666.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1840 9.9 %RANDOM
Rwork0.184 ---
all-18672 --
obs-18672 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.5434 Å2 / ksol: 0.418904 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2---2.6 Å20 Å2
3---0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 75 224 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.672
X-RAY DIFFRACTIONc_scangle_it3.582.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 310 10.1 %
Rwork0.204 2754 -
obs--100 %
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: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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