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- PDB-3e4q: Crystal structure of apo DctB -

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Basic information

Entry
Database: PDB / ID: 3e4q
TitleCrystal structure of apo 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
C4-dicarboxylate transport sensor protein DctB
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)66,1294
Polymers66,0492
Non-polymers802
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-37 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.988, 38.735, 111.172
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C4-dicarboxylate transport sensor protein dctB


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES PH 7.5, 15-20% PEG 3350, 0.04M CALCIUM CHLORIDE, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 12743 / % possible obs: 95.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.369 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3E4O

3e4o


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 37.097 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 663 5.2 %RANDOM
Rwork0.195 ---
obs0.199 11984 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å22.18 Å2
2--2.08 Å20 Å2
3----2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 2 10 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223956
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.291.9865380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1025506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08422.073164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.39815640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6751546
X-RAY DIFFRACTIONr_chiral_restr0.2090.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.21942
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.22702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7781.52577
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33324066
X-RAY DIFFRACTIONr_scbond_it2.18231535
X-RAY DIFFRACTIONr_scangle_it3.5414.51314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 42 -
Rwork0.273 884 -
obs--97.89 %
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)
13.4297-1.1137-0.85152.00390.94554.7546-0.0294-0.13240.03650.1501-0.00870.0012-0.01170.22420.0381-0.1958-0.03350.0057-0.20660.0436-0.186123.65610.116741.2877
23.7252-2.1896-0.66133.23971.0523.69740.11420.28810.1222-0.2464-0.16010.3951-0.3025-0.42530.0459-0.0980.01260.0228-0.21580.0184-0.108213.60173.250113.9865
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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