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- PDB-3e4o: Crystal structure of succinate bound state DctB -

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Basic information

Entry
Database: PDB / ID: 3e4o
TitleCrystal structure of succinate bound state 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
SUCCINIC ACID / C4-dicarboxylate transport sensor protein DctB
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 1.2Oct 25, 2017Group: Refinement description / Category: software

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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)66,9916
Polymers66,7062
Non-polymers2854
Water3,585199
1
A: C4-dicarboxylate transport sensor protein dctB
hetero molecules

A: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2278
Polymers66,7062
Non-polymers5216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1890 Å2
ΔGint-18 kcal/mol
Surface area23840 Å2
MethodPISA
2
B: C4-dicarboxylate transport sensor protein dctB
hetero molecules

B: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7544
Polymers66,7062
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1900 Å2
ΔGint-17 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.892, 66.594, 93.602
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33352.875 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6
Details: 0.6M SODIUM SUCCINATE PH 6.0, 3% TRIFLUROETHANOL, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9760, 0.9799, 0.9796
DetectorType: MAR345DTB / Detector: CCD / Date: Aug 24, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.97991
30.97961
ReflectionResolution: 2.3→50 Å / Num. obs: 27795 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.25 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.316 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1299 4.7 %RANDOM
Rwork0.2 ---
obs0.203 26441 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.13 Å2
2---0.71 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 18 199 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.995409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2815506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24321.951164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82715646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6541547
X-RAY DIFFRACTIONr_chiral_restr0.1250.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023037
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21717
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22657
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7161.52621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13124074
X-RAY DIFFRACTIONr_scbond_it1.83631555
X-RAY DIFFRACTIONr_scangle_it2.9684.51335
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
Rwork0.253 1926 -
obs--100 %
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)
11.13410.325-0.23983.14790.65411.03870.0789-0.0815-0.00130.1697-0.0293-0.0278-0.03410.0389-0.0496-0.17390.00620.0052-0.15840.033-0.059514.7266.2326.728
21.011-0.06540.03573.25581.51231.9804-0.04610.03640.0314-0.11280.0999-0.02670.03550.1734-0.0538-0.1269-0.0208-0.0319-0.07490.0613-0.060511.21682.52739.577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA56 - 30849 - 301
2X-RAY DIFFRACTION2BB56 - 30849 - 301

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