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- PDB-1m5t: CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK -

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Basic information

Entry
Database: PDB / ID: 1m5t
TitleCRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK
Componentscell division response regulator DivK
KeywordsSIGNALING PROTEIN / CELL CYCLE / RESPONSE REGULATOR / SIGNAL TRANSDUCTION PROTEIN / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


phosphorelay signal transduction system / metal ion binding
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polar differentiation response regulator
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsGuillet, V. / Ohta, N. / Cabantous, S. / Newton, A. / Samama, J.-P. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystallographic and biochemical studies of DivK reveal novel features of an essential response regulator in Caulobacter crescentus
Authors: Guillet, V. / Ohta, N. / Cabantous, S. / Newton, A. / Samama, J.-P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Characterization and Crystallization of Divk, an Essential Response Regulator for Cell Division and Differentiation in Caulobacter Crescentus
Authors: Cabantous, S. / Guillet, V. / Ohta, N. / Newton, A. / Samama, J.-P.
#2: Journal: Embo J. / Year: 1995
Title: An Essential Single Domain Response Regulator Required for Normal Cell Division and Differentiation in Caulobacter Crescentus
Authors: Hecht, G.B. / Lane, T. / Ohta, N. / Sommer, J.M. / Newton, A.
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cell division response regulator DivK


Theoretical massNumber of molelcules
Total (without water)14,0591
Polymers14,0591
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.210, 40.350, 67.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein cell division response regulator DivK / polar differentiation response regulator / CheY homolog DivK


Mass: 14059.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE AT PH 6.0 IN THE APO-FORM / Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: divk / Plasmid: PT7-7 PZHF55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-PLYSS / References: UniProt: Q9A5I4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.8 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging or sitting-drop / pH: 6
Details: MES 50mM PH6.0, PEG MME 550 32% AT 285K, The Protein was Concentrated At 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing ...Details: MES 50mM PH6.0, PEG MME 550 32% AT 285K, The Protein was Concentrated At 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing PEG MME 550 (32%), MES PH 6.00 (40 mM), DTT (5 mM). Crystal Size (300X40X40 microM3) In 20 microL Sitting Drops. Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In PEG MME 550 (50%), MES PH 6.00 (40 mM). VAPOR DIFFUSION, HANGING OR SITTING-DROP at 285K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Details: Cabantous, S., (2002) Acta Crystallogr., Sect.D, 58, 1249.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
220 mMMES/NaOH1droppH6.0
35 mMdithiothreitol1drop
432 %PEG550 MME1reservoir
540 mMMES1reservoirpH6.0
65 mMdithiothreitol1reservoir
70.01 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.946 / Wavelength: 0.946 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 1999
RadiationMonochromator: Si111 or Si311 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 13114 / Num. obs: 13114 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 5.8 / Num. unique all: 4364 / % possible all: 83
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. measured all: 58069 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 83 % / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: APO-DIVK SOLVED AT PH7

Resolution: 1.6→10 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1328 10.3 %RANDOM
Rwork0.193 ---
all0.193 13114 --
obs0.193 12888 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9843 Å2 / ksol: 0.381409 e/Å3
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å20 Å2
2--3.07 Å20 Å2
3----0.18 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 0 120 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it0.681.5
X-RAY DIFFRACTIONc_mcangle_it1.062
X-RAY DIFFRACTIONc_scbond_it1.222
X-RAY DIFFRACTIONc_scangle_it1.782.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 184 10.4 %
Rwork0.21 1591 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Rfactor obs: 0.193 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.21

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