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- PDB-2zbb: P43 crystal of DctBp -

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Basic information

Entry
Database: PDB / ID: 2zbb
TitleP43 crystal of DctBp
ComponentsC4-dicarboxylate transport sensor protein dctB
KeywordsTRANSFERASE / PAS / periplasmic histidine kinase / Inner membrane / Membrane / Phosphorylation / Transmembrane / Two-component regulatory system
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 / C4-dicarboxylate transport sensor protein DctB
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhou, Y.F. / Nan, B.Y. / Liu, X. / Nan, J. / Liang, Y.H. / Panjikar, S. / Ma, Q.J. / Wang, Y.P. / Su, X.-D.
CitationJournal: to be published
Title: crystal structures of sensory histidine kinase DctBp
Authors: Zhou, Y.F. / Nan, B.Y. / Liu, X. / Nan, J. / Liang, Y.H. / Panjikar, S. / Ma, Q.J. / Wang, Y.P. / Su, X.-D.
History
DepositionOct 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
C: C4-dicarboxylate transport sensor protein dctB
D: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4548
Polymers132,0384
Non-polymers4164
Water28816
1
A: C4-dicarboxylate transport sensor protein dctB
B: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2274
Polymers66,0192
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-28 kcal/mol
Surface area23390 Å2
MethodPISA
2
C: C4-dicarboxylate transport sensor protein dctB
D: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2274
Polymers66,0192
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-26 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 70.360, 226.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
C4-dicarboxylate transport sensor protein dctB


Mass: 33009.535 Da / Num. of mol.: 4 / Fragment: periplasmic sensing domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium 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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREFERENCE FOR THE POSITION 309 (K -> N) IS FEMS MICROBIOLOGY LETTERS 14 (1982) 95-99, DEREPRESSION ...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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M sodium malonate pH 6.0, 13%-15% PEG 3350, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9875 Å
DetectorType: Mar / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 37598
Reflection shellResolution: 2.5→20 Å

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.427 / Cor.coef. Fo:Fc: 0.576
Highest resolutionLowest resolution
Rotation3 Å19.68 Å
Translation3 Å19.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.03 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.64 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27226 1874 5 %RANDOM
Rwork0.20938 ---
obs0.21251 35620 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: 47.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.45 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 28 16 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0227717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4481.98410516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.15251016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38522.241299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.601151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4681579
X-RAY DIFFRACTIONr_chiral_restr0.1870.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.23663
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.25210
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3850.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.55235
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25628056
X-RAY DIFFRACTIONr_scbond_it2.18232850
X-RAY DIFFRACTIONr_scangle_it3.424.52460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 134 -
Rwork0.32 2557 -
all-2691 -
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)
11.28580.7577-0.78418.0162-0.86541.5101-0.1602-0.53090.05520.3350.02910.19370.00030.04490.1311-0.28260.0686-0.0150.0689-0.0699-0.179-18.60417.19470.1443
23.40610.6902-0.5174.6054-1.06095.0629-0.19820.18140.0734-0.4766-0.1316-0.02240.7082-0.23660.3298-0.2181-0.08960.071-0.14880.0046-0.237-14.80548.0899-27.8246
31.8552-0.22990.75727.34712.68877.10850.14230.17690.0614-0.0664-0.2517-0.1627-0.47450.21040.1094-0.2961-0.0771-0.0178-0.13510.0176-0.21218.035333.5576-28.8148
43.3105-2.57150.06165.68170.74923.36470.16080.2285-0.33760.1094-0.34010.47030.11610.03190.1794-0.2658-0.0190.0019-0.0781-0.1164-0.180215.44432.9638-0.297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA54 - 30847 - 301
2X-RAY DIFFRACTION2BB54 - 30847 - 301
3X-RAY DIFFRACTION3CC54 - 30847 - 301
4X-RAY DIFFRACTION4DD54 - 30847 - 301

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