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- PDB-3e4p: Crystal structure of malonate occupied DctB -

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Basic information

Entry
Database: PDB / ID: 3e4p
TitleCrystal structure of malonate occupied DctB
ComponentsC4-dicarboxylate transport sensor protein dctB
KeywordsTRANSFERASE / PAS DOMAIN / N-TERM HELICAL DIMERIZATION DOMAIN
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3020 / Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3020 / Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Helix non-globular / Histidine kinase/HSP90-like ATPase superfamily / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / STRONTIUM ION / C4-dicarboxylate transport sensor protein DctB
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, Y.F. / Nan, J. / Nan, B.Y. / Liang, Y.H. / Panjikar, S. / Su, X.D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain.
Authors: Zhou, Y.F. / Nan, B.Y. / Nan, J. / Ma, Q.J. / Panjikar, S. / Liang, Y.H. / Wang, Y.P. / Su, X.D.
History
DepositionAug 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: C4-dicarboxylate transport sensor protein dctB
B: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5207
Polymers66,0492
Non-polymers4715
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-133 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.980, 39.100, 111.540
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C4-dicarboxylate transport sensor protein dctB / sensory histidine kinase


Mass: 33024.613 Da / Num. of mol.: 2 / Fragment: periplasmic sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: dctB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13633, histidine kinase
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (DCTB_RHIME P13633) SHOWS CONFLICT AT THE POSITION 174: N -> K (IN REF. 5). ...THE FEATURE OF UNIPROT (DCTB_RHIME P13633) SHOWS CONFLICT AT THE POSITION 174: N -> K (IN REF. 5). REFERENCE FOR THE POSITION 309 (K -> N) IS FEMS MICROBIOLOGY LETTERS 14 (1982) 95-99, DEREPRESSION OF RIBULOSE BISPHOSPHATE CARBOXYLASE ACTIVITY IN RHIZOBIUM MELILOTI SUNDARAM S. MANIAN AND FERGAL O'GARA

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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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6
Details: 0.2 M SODIUM MALONATE PH 6.0, 13-15% PEG 3350, 5-10 mM STRONTIUM CHLORIDE, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→30.5 Å / Num. obs: 22061 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.49 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.12
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / % possible all: 94.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3E4P

3e4p


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.189 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1142 5.2 %RANDOM
Rwork0.196 ---
obs0.199 20919 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.02 Å2
2--2.28 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 17 113 3984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9875336
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58221.824159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02715624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1861546
X-RAY DIFFRACTIONr_chiral_restr0.110.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22619
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6771.52522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25624036
X-RAY DIFFRACTIONr_scbond_it2.19831454
X-RAY DIFFRACTIONr_scangle_it3.5444.51300
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 84 -
Rwork0.245 1424 -
obs--93.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0114-0.5469-0.60780.49550.53482.3003-0.0196-0.0245-0.09750.0829-0.06610.0719-0.0180.10190.0857-0.0601-0.0169-0.0016-0.10980.0085-0.089623.46270.103841.3516
22.0757-1.0827-0.02831.92440.6892.38870.07890.14090.0541-0.1205-0.1270.1987-0.1649-0.22640.048-0.08010.0279-0.0081-0.0910.0071-0.067613.75513.236613.9486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA56 - 30549 - 298
2X-RAY DIFFRACTION2BB56 - 30549 - 298

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