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- PDB-1m5u: CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH... -

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Basic information

Entry
Database: PDB / ID: 1m5u
TitleCRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH 8.0 IN THE APO-FORM
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: 1.87 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

Downloads & links

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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
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.670, 40.710, 66.290
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 8.0 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


Mass: 18.015 Da / Num. of mol.: 64 / 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: 8
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 (5mM). Crystal Size (300X40X40 microM3) In 20microL Sitting Drops. VAPOR DIFFUSION, HANGING OR SITTING-DROP at 285K. Crystals Were Transferred In Reservoir Solutions Whose Ph Was Increased From 6.0 To 8.0 By Steps Of 0.5 Ph Units (The Soaking Time In Each Solution Was 12 Hours). Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In Peg Mme 550 (50%), Tris Ph 8.0 (40 Mm)., pH 8.00
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: BM30A / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2000
RadiationMonochromator: Si111 or Si311 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.87→35 Å / Num. all: 8414 / Num. obs: 8414 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.3
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 7.9 / Num. unique all: 5050 / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 42648 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: APO-DIVK SOLVED AT PH6

Resolution: 1.87→15 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.206 854 10.6 %RANDOM
Rwork0.19 ---
all0.1901 8414 --
obs0.1901 8022 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 111.642 Å2 / ksol: 0.524279 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--1.45 Å20 Å2
3----1.38 Å2
Refine analyzeLuzzati coordinate error free: 0.22 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.87→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 64 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.412.5
LS refinement shellResolution: 1.87→1.99 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 127 10.8 %
Rwork0.184 1044 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refinement
*PLUS
Rfactor obs: 0.1901 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.253 / Rfactor Rwork: 0.184

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