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- PDB-1qkk: Crystal structure of the receiver domain and linker region of Dct... -

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Basic information

Entry
Database: PDB / ID: 1qkk
TitleCrystal structure of the receiver domain and linker region of DctD from Sinorhizobium meliloti
ComponentsC4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsTRANSCRIPTIONAL REGULATORY PROTEIN / RECEIVER DOMAIN / 2-COMPONENT SIGNAL TRANSDUCTION / SIGMA-54 DEPENDENT TRANSCRIPTIONAL ACTIVATOR / BACTERIAL ENHANCER BINDING PROTEIN / HIGH SOLVENT CONTENT CRYSTAL
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 / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsMeyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / Mckinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Farber, G.K. / Nixon, B.T.
Citation
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.
#1: Journal: Science / Year: 1987
Title: Crystallographic R Factor Refinement by Molecular Dynamics
Authors: Brunger, A.T. / Kuriyan, J. / Karplus, M.
History
DepositionJul 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,8211
Polymers16,8211
Non-polymers00
Water3,675204
1
A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,6432
Polymers33,6432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.651, 58.769, 167.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTHE MOLECULE EXISTS AS A DIMER IN SOLUTION . THE DIMER ISCOMPRISED OF MONOMERS FROM DIFFERENT UNIT CELLS.DIMERIZATION SURFACES OCCUR AT THE FACES OF THE UNIT CELL"BOX".

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Components

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


Mass: 16821.260 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 TO 143, RECEIVER DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS EXPRESSED WITH THE C-TERMINAL HIS-TAG, KLAAALEHHHHHH. COORDINATES ARE SUBMITTED ONLY FOR THE MONOMER, WHICH COMPRISES THE COMPLETE ASYMMETRIC UNIT.
Source: (gene. exp.) SINORHIZOBIUM MELILOTI (bacteria) / Strain: N.A. 1021 / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): B834 PLYSS / References: UniProt: P13632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A: RESIDUES 144 TO 156 ARE A HIS TAG
Source detailsTHE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., ...THE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., CONSERVATION BETWEEN CODING AND REGULATORY ELEMENTS OF RHIZOBIUM MELILOTI AND RHIZOBIUM LEGUMINOSARUM DCT GENES, J. BACTERIOL. 171:5244-5253(1989). THE SWISSPROT ENTRY, P13632/DCTD_RHIME DESCRIBES THE SEQUENCE FROM N.A. STRAIN=JJ1C10 REFERENCE: WATSON R.J., ANALYSIS OF THE C4-DICARBOXYLATE TRANSPORT GENES OF RHIZOBIUM MELILOTI: NUCLEOTIDE SEQUENCE AND DEDUCED PRODUCTS OF DCTA, DCTB, AND DCTD, MOL. PLANT MICROBE INTERACT. 3:174-181(1990). THE TWO VARIANTS DIFFER AT THE FOLLOWING RESIDUES N.A. 1021 (THIS WORK) N.A. JJ1C10 (P13632) SEQ: 43 GLY GLU SEQ: 68 ARG GLY SEQ: 70 ILE VAL THE N-TERMINAL MET RESIDUE IS CLEAVED IN VIVO.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 %
Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON ...Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON SOURCE.THESE FACILITIES ARE SUPPORTED BY THE COMPANIES OF THE INDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION THROUGH A CONTRACT WITH ILLINOIS INSTITUTE OF TECHNOLOGY (IIT), EXECUTED THROUGH THE IIT'S CENTER FOR SYNCHROTRON RADIATION RESEARCH AND INSTRUMENTATION.
Crystal growpH: 5.6
Details: 50 MM NA SUCCINATE PH 5.6, 70 MM AMMONIUM PHOSPHATE MONOBASIC, 1 MM DTT
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
250 mMsuccinate1reservoir
375 mM1reservoirNH4H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.98333, 0.98100, 0.98076
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 1998 / Details: NO FOCUSSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (111) MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.983331
20.9811
30.980761
ReflectionResolution: 1.7→20 Å / Num. obs: 61207 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.062 / Net I/σ(I): 34
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.324 / % possible all: 100
Reflection
*PLUS
Num. obs: 32439 / % possible obs: 86.1 % / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
CNS0.9refinement
HKL-2000(DENZO)data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1822253.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2778 9.9 %RANDOM
Rwork0.218 ---
obs0.218 27943 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1063 Å2 / ksol: 0.415432 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å20 Å20 Å2
2--0.87 Å20 Å2
3---2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.01 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 0 204 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 324 10 %
Rwork0.213 2908 -
obs--60.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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