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- PDB-1mb0: CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK AT PH 8.0 IN COM... -

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Basic information

Entry
Database: PDB / ID: 1mb0
TitleCRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK AT PH 8.0 IN COMPLEX WITH MN2+
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: 2 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
DepositionAug 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jan 24, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1693
Polymers14,0591
Non-polymers1102
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.120, 40.760, 66.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cell division response regulator DivK / Polar differentiation response regulator / DIVK RESPONSE REGULATOR


Mass: 14059.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: divk / Plasmid details: PT7-7, T7 PROMOTOR / Plasmid: PZHF55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-PLYSS / References: UniProt: Q9A5I4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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 (5 mM). Crystal Size (300X40X40 microM3) In 20microL Sitting Drops. Crystals 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). Manganese Derivative Was Obtained By Soaking For 24 Hours Protein Crystals In The Reservoir Solution Supplemented With 10 Mm MnCl2 (PH 8.00). Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In Peg MME 550 (50%), Tris PH 8.0 (40 Mm)., VAPOR DIFFUSION, HANGING OR SITTING-DROP
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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 16, 2000
RadiationMonochromator: Si111 or Si311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. obs: 6829 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2970 / % possible all: 98.2
Reflection
*PLUS
Lowest resolution: 27 Å / Redundancy: 3 % / Num. measured all: 20270
Reflection shell
*PLUS
% possible obs: 98.2 % / Mean I/σ(I) obs: 2.7

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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 PH6

Resolution: 2→14.95 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 649 11.1 %RANDOM
Rwork0.208 ---
all-6829 --
obs-6829 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.0755 Å2 / ksol: 0.353232 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2--1 Å20 Å2
3----3.74 Å2
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 2 37 866
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.332
X-RAY DIFFRACTIONc_scangle_it2.032.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 103 12.9 %
Rwork0.238 697 -
obs--70.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Num. reflection obs: 5224 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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