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- PDB-4q20: Crystal structure of a C-terminal part of tyrosine kinase (DivL) ... -

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Basic information

Entry
Database: PDB / ID: 4q20
TitleCrystal structure of a C-terminal part of tyrosine kinase (DivL) from Caulobacter crescentus CB15 at 2.50 A resolution (PSI Community Target, Shapiro)
ComponentsSensor protein DivL
KeywordsTRANSFERASE / Signal transduction / two-component regulatory system / HisKA domain / GHKL domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Plos Biol. / Year: 2014
Title: Cell fate regulation governed by a repurposed bacterial histidine kinase.
Authors: Childers, W.S. / Xu, Q. / Mann, T.H. / Mathews, I.I. / Blair, J.A. / Deacon, A.M. / Shapiro, L.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 23, 2014ID: 4EW8
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein DivL
B: Sensor protein DivL


Theoretical massNumber of molelcules
Total (without water)57,7292
Polymers57,7292
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.530, 69.530, 194.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sensor protein DivL


Mass: 28864.488 Da / Num. of mol.: 2 / Fragment: Histidine kinase domain residues 523-769
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: divL, CC_3484 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RQQ9, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 523-769) WAS EXPRESSED WITH A PURIFICATION TAG MGSSHHHHHHSSGLVPRGSHM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3547.66THE STRUCTURE WAS SOLVED USING FOUR WAVELENGTH MAD PHASES FROM A HEAVY ATOM (AU) DERIVATIVE OF ANOTHER CRYSTAL. THE PHASING CRYSTAL DIFFRACTED TO 3.2 A. TO OBTAIN HEAVY ATOM DERIVATIVES, CRYSTALS WERE SOAKED IN CRYO SOLUTION CONTAINING 0.01 M POTASSIUM DICYANOAURATE FOR 10 MINUTES.
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 10K, 0.1 M HEPES pH 7.5, MG and ADP, both at 5 mM concentrations, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL12-221.0397,0.8731,1.04,1.0436
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELApr 25, 2011Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
DECTRIS PILATUS 6M2PIXELMar 28, 2011Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)MADMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.03971
30.87311
41.041
51.04361
ReflectionResolution: 2.5→44.112 Å / Num. obs: 19457 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 87.218 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 27.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.60.0112.11478421021,299
2.6-2.690.0113.51237216601,299.5
2.69-2.80.0115.71212517141,298.7
2.8-2.930.0118.81293117381,299.5
2.93-3.080.01112.51278716681,299.6
3.08-3.270.01118.41266217061,299.8
3.27-3.520.011301253117221,299.4
3.52-3.880.01141.61168617731,299.2
3.88-4.430.01154.41211917121,299.7
4.43-5.570.01157.31119417781,298.6
5.57-44.110.01163.61206618841,297.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→44.112 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9501 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU R CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT (AUTONCS). 3. DUE ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU R CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT (AUTONCS). 3. DUE TO AMBIGUITY IN THE DENSITY OF THE LINKER 570-573, THE N-TERMINAL FRAGMENT OF EACH MONOMER CANNOT BE ASSIGNED UNIQUELY TO ONE MONOMER. THE CHAIN ASSIGNMENT WAS CHOSEN SUCH THAT THE CONNECTIVITY IN A MONOMER IS THE SAME AS OTHER HOMOLOGOUS HISTIDINE KINASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 965 4.96 %RANDOM
Rwork0.2017 ---
obs0.2032 19452 99.14 %-
Displacement parametersBiso max: 205.81 Å2 / Biso mean: 107.0939 Å2 / Biso min: 56.24 Å2
Baniso -1Baniso -2Baniso -3
1--5.2702 Å20 Å20 Å2
2---5.2702 Å20 Å2
3---10.5404 Å2
Refine analyzeLuzzati coordinate error obs: 0.538 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 0 19 3425
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1632SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes519HARMONIC5
X-RAY DIFFRACTIONt_it3451HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion451SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3728SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3451HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4674HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion2.83
LS refinement shellResolution: 2.5→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2702 132 4.78 %
Rwork0.2343 2630 -
all0.2359 2762 -
obs--99.14 %
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)
11.77960.5904-0.17333.89921.4443.658-0.1106-0.09710.21170.22530.07640.0532-0.3598-0.40710.03420.00480.2056-0.0127-0.11540.0024-0.11510.605941.519754.474
23.6734-1.0398-1.98782.9942-1.35154.6114-0.09570.2891-0.0195-0.0284-0.19980.08730.1994-0.03210.2955-0.08450.1059-0.0372-0.0447-0.0081-0.168411.492133.180641.2047
35.18260.68763.0854.9953-0.12945.61390.33690.153-0.7327-0.53580.09640.20540.576-0.2959-0.43330.04070.1301-0.1985-0.24960.03980.13587.905242.968727.7129
42.3776-0.4797-0.6243.77141.2893.0167-0.1156-0.18380.21550.18530.1931-0.16070.00340.426-0.0776-0.07610.1386-0.03730.0045-0.027-0.163619.179835.857648.5807
53.5369-0.2231-0.60720.6466-1.68863.2084-0.235-0.6022-0.14220.28540.1795-0.21230.5085-0.23110.0554-0.01380.2145-0.0468-0.08720.0406-0.29313.615326.817255.4725
67.99250.367-1.39698.013-1.96856.50960.2573-0.2999-0.68120.2648-0.32730.09130.285-0.46390.07-0.2516-0.1451-0.16380.04130.04-0.30422.890124.612772.5616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|526 - 570}A526 - 570
2X-RAY DIFFRACTION2{A|573 - 609}A573 - 609
3X-RAY DIFFRACTION3{A|610 - 758}A610 - 758
4X-RAY DIFFRACTION4{B|526 - 570}B526 - 570
5X-RAY DIFFRACTION5{B|573 - 609}B573 - 609
6X-RAY DIFFRACTION6{B|610 - 756}B610 - 756

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