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- PDB-8a3u: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (symme... -

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Basic information

Entry
Database: PDB / ID: 8a3u
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1 (symmetrical variant, trigonal form with short c-axis)
ComponentsPutative Sensory box protein,Sensor protein FixL
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor / sensory histidine kinase / chimeric / De Novo Protein
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase-related protein, C-terminal ...: / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN MONONUCLEOTIDE / Sensor protein FixL / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
Bradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsArinkin, V. / Batra-Safferling, R. / Granzin, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchOptoSys, FKZ 031A16 Germany
CitationJournal: To Be Published
Title: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (symmetrical variant, trigonal form with short c-axis)
Authors: Arinkin, V. / Batra-Safferling, R. / Granzin, J. / Krauss, U.
History
DepositionJun 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Sensory box protein,Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3323
Polymers43,3691
Non-polymers9642
Water00
1
A: Putative Sensory box protein,Sensor protein FixL
hetero molecules

A: Putative Sensory box protein,Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6656
Polymers86,7382
Non-polymers1,9274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area12390 Å2
ΔGint-79 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.716, 138.716, 49.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Putative Sensory box protein,Sensor protein FixL


Mass: 43368.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; belongs to Q88JB0: 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120); belongs to P23222:141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368); UNP:Q88JB0 ...Details: His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; belongs to Q88JB0: 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120); belongs to P23222:141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368); UNP:Q88JB0 (UNP-numbering) 4-(MSE)INA...QRDVT-123; UNP:P23222 (UNP-numbering) 258 to C-Term. Expression system: because of SeMet: E.coli B834 (DE3).
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria), (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440, JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110
Gene: PP_2739, fixL, bll2760 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q88JB0, UniProt: P23222, histidine kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG8K, 0.1M Citrate, 0.2M NaCl, 0.1M Ammonium Bromide, 1mM ATP, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 13, 2015
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.33→45.65 Å / Num. obs: 13863 / % possible obs: 58.6 % / Redundancy: 20 % / Biso Wilson estimate: 75.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.027 / Rrim(I) all: 0.12 / Net I/σ(I): 19.8
Reflection shellResolution: 2.33→2.51 Å / Rmerge(I) obs: 2.26 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 693 / CC1/2: 0.48 / Rpim(I) all: 0.549 / % possible all: 14.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→45.65 Å / SU ML: 0.4343 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 40.4131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (13861 reflections). However, separating the ...Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (13861 reflections). However, separating the reflections on F(+) and F(-), the Phenix program gives a number of 26710 reflections for the refinement. The statistics (number of reflections) in resolution shells also refers to F(+) and F(-). Attention, these are very strong anisotropic data, so that the spherical completeness is relatively low.
RfactorNum. reflection% reflection
Rfree0.2797 651 4.66 %
Rwork0.232 25464 -
obs0.2341 13861 58.58 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.42 Å2
Refinement stepCycle: LAST / Resolution: 2.33→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 62 0 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242935
X-RAY DIFFRACTIONf_angle_d0.81883979
X-RAY DIFFRACTIONf_chiral_restr0.0628445
X-RAY DIFFRACTIONf_plane_restr0.0066526
X-RAY DIFFRACTIONf_dihedral_angle_d13.22751123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.510.4064740.38681235X-RAY DIFFRACTION14.37
2.51-2.760.37931780.37643250X-RAY DIFFRACTION37.64
2.76-3.160.39312150.32924964X-RAY DIFFRACTION56.98
3.16-3.980.32153760.26327311X-RAY DIFFRACTION84.08
3.98-45.650.23734030.19668704X-RAY DIFFRACTION99.9
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)
14.734830144230.648195399421-0.05256977481284.95866447564-1.931147265746.097103761690.1304029204740.1120424231260.4645171282460.00964651203740.2456404194120.416373277537-0.555075584975-1.32680795345-0.3168413838640.2921546219250.06852405292650.09956540011170.598104493760.07797507842770.480001733531-29.53660448549.269327013413.24202514089
22.022190073072.3086197627-0.841726256788-0.0524054776761-0.2553800747380.603858016699-0.0526531889777-0.7676444660280.1039279451670.141652914489-0.366625868615-0.196676058001-0.3369480775521.075291136490.3144894786020.417402402633-0.121446754662-0.05422062518991.66273884999-0.03872862024651.10377147147-87.0305692924-1.783354549763.05989708328
37.67562154344-2.12237245937-1.074203267551.611985721770.9124978728171.513122106190.1481693931831.75717720544-1.10720325197-0.219366442725-0.30098720068-0.4983215752370.4851426799080.9886282634370.1443637285150.9418579812630.06331744591540.0115891389071.89837466891-0.09436428035881.48944473425-75.842720352-13.04451793671.64037293233
43.264035929881.209889135240.009911401958642.00044851268-2.427413718085.63588120963-0.1994796984830.573497408102-0.6736259080660.2446953164790.232495579691-0.4652230056110.3039287384510.146220773061-0.03457000716781.290704796920.319761456967-0.07210759238692.127036861660.08791703153642.37309290581-75.5416936838-15.702931524710.5283262976
52.00236731535.485747026182.163259404595.931772854016.837792310082.002035242510.08689727855650.1203956123740.70135855222-0.714501209019-0.2203123683390.877031851556-1.1166110998-1.419150754360.1565193341330.4647565596070.347366381070.1917569475351.007017270630.02868105214330.583122046889-33.431759879615.09449925412.98869046341
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 119 )A-1 - 1191 - 121
22chain 'A' and (resid 120 through 179 )A120 - 179122 - 181
33chain 'A' and (resid 180 through 362 )A180 - 362182 - 364
44chain 'A' and (resid 401 through 401 )B401
55chain 'A' and (resid 402 through 402 )C402

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