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- PDB-8a7h: Crystal structure of a chimeric LOV-Histidine kinase SB2F1-I66R m... -

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Basic information

Entry
Database: PDB / ID: 8a7h
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1-I66R mutant (light state; asymmetrical variant, trigonal form with long 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 / nucleotide binding / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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 ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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. / 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 (semi-quinone intermediate) / Sensor protein FixL / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
Bradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.145 Å
AuthorsArinkin, V. / Granzin, J. / Batra-Safferling, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 031A16 Germany
CitationJournal: To Be Published
Title: Crystal structure of a chimeric LOV-Histidine kinase SB2F1-I66R mutant (light state; asymmetrical variant, trigonal form with long c axis)
Authors: Arinkin, V. / Granzin, J. / Batra-Safferling, R. / Krauss, U.
History
DepositionJun 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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


Theoretical massNumber of molelcules
Total (without water)87,8196
Polymers85,8882
Non-polymers1,9314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-76 kcal/mol
Surface area35410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.420, 139.420, 89.881
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLEUA1 - 362
d_12ens_1ATPATPB
d_13ens_1GEDGEDC
d_21ens_1METLEUD1 - 362
d_22ens_1ATPATPE
d_23ens_1GEDGEDF

NCS oper: (Code: givenMatrix: (-0.494528640582, -0.868140585722, -0.0421111275879), (-0.868185915362, 0.49109878248, 0.0712404534909), (-0.0411660055334, 0.0717907324711, -0.996569842369)Vector: 5. ...NCS oper: (Code: given
Matrix: (-0.494528640582, -0.868140585722, -0.0421111275879), (-0.868185915362, 0.49109878248, 0.0712404534909), (-0.0411660055334, 0.0717907324711, -0.996569842369)
Vector: 5.10332466873, 5.16682508366, -11.6740494863)

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Components

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


Mass: 42944.027 Da / Num. of mol.: 2 / Mutation: I66R
Source method: isolated from a genetically manipulated source
Details: HIS-TAG: 1-MGSSHHHHHHSSGLVPRGSH-20; BELONGS TO Q88JB0: 21 (OR 1 PDB-FILE)-MINA...YYIGIQRDVT-140 (OR 120); BELONGS TO P23222:141 (OR 121 PDB-FILE)-EHQQTQ...AADEN-388 (OR 368); UNP:Q88JB0 (UNP- ...Details: HIS-TAG: 1-MGSSHHHHHHSSGLVPRGSH-20; BELONGS TO Q88JB0: 21 (OR 1 PDB-FILE)-MINA...YYIGIQRDVT-140 (OR 120); BELONGS TO P23222:141 (OR 121 PDB-FILE)-EHQQTQ...AADEN-388 (OR 368); UNP:Q88JB0 (UNP-NUMBERING) 4-MINA...QRDVT-123; UNP:P23222 (UNP-NUMBERING) 258 TO C-TERM; ENGINEERED MUTATION: ILE 66 ARG.
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria), (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88JB0, UniProt: P23222, histidine kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-JGC / Flavin mononucleotide (semi-quinone intermediate) / [(2R,3S,4S)-5-[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-4a,5-dihydrobenzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 18% PEG3300, 0.1M Bicine, 0.2M LiSO4, 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2016
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.145→45.64 Å / Num. obs: 12416 / % possible obs: 69.6 % / Redundancy: 19.7 % / Biso Wilson estimate: 109.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.038 / Rrim(I) all: 0.168 / Net I/σ(I): 12.5
Reflection shellResolution: 3.145→3.336 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 621 / CC1/2: 0.483 / Rpim(I) all: 0.61 / % possible all: 21.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292121855

Resolution: 3.145→45.64 Å / SU ML: 0.4374 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.5547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Attention, these are very strong anisotropic data, so that the spherical completeness is relatively low. In the revision, I would like to compare the spherical resolution with the ellipsoidal resolution.
RfactorNum. reflection% reflection
Rfree0.3056 977 7.87 %
Rwork0.2533 11435 -
obs0.2574 12416 69.54 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104 Å2
Refinement stepCycle: LAST / Resolution: 3.145→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 124 0 5756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535842
X-RAY DIFFRACTIONf_angle_d0.86077918
X-RAY DIFFRACTIONf_chiral_restr0.0537886
X-RAY DIFFRACTIONf_plane_restr0.00561050
X-RAY DIFFRACTIONf_dihedral_angle_d14.45842218
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.82166923039 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.145-3.460.4648930.36691116X-RAY DIFFRACTION27.43
3.46-3.960.35231970.3312453X-RAY DIFFRACTION60.04
3.96-4.990.33343520.27133621X-RAY DIFFRACTION89.56
4.99-45.640.27083350.22234245X-RAY DIFFRACTION99.91
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)
11.81758024263-1.53953489994-0.3708328739193.40880321781-0.346088318425-0.015260752290.1039158991940.220512856448-0.22448271806-0.617354848112-0.1683964065340.4679156224360.0727066820185-0.1098066518180.1236995495310.805752910745-0.0996860087066-0.2691628161420.452982583208-0.04551822701540.46154247705321.1467930739-43.326760992-12.4781840193
22.40542335476-1.896764265360.2370299435899.94207368362-2.009042135870.4116318169310.0265998853840.08108338011050.221020294053-1.48323990129-0.00249596602947-0.601280604740.163872049734-0.0143410713596-0.0940007816820.988437267546-0.06728990594490.05766277297910.675700309977-0.1202233346390.53370526463753.6813111018-58.5941802404-14.4539730325
39.798606703548.226326587358.904748851992.000715296855.364986795671.999716767620.76632330331-2.265096987970.434516728462.16286848436-1.652318504320.7880398628480.538648903173-0.7832133601190.8376940341521.14378486107-0.2385093207150.138464893280.880494829915-0.04163929525060.70606381839355.1011191267-56.5815246246-5.71063735992
42.001078047451.99985698318-2.889258855792.0000601996-3.892095523534.98911752923-0.2000838808030.347434965945-0.201602957094-0.4677169982120.174500280749-0.2491475338460.1019650262410.02454390800260.08699190034380.655478796748-0.0657032222799-0.5778914712460.8740010591470.3624647724630.7971261031347.06657545252-37.0749273065-11.3549603024
53.65389467242-0.584327637887-0.6834833862962.723619700090.8449392692571.837482158790.343580071035-0.5497888632841.063037021830.147792407480.134404814555-0.312074405622-0.05177784852250.38839967614-0.3914423137570.62534734722-0.123174402708-0.08330281417960.605442501561-0.1690068410880.8110402900926.168313647-19.7397523401-2.27257748557
61.52223196889-2.892525231630.9441319588587.90466475678-0.908086449281.57879545708-0.485220502002-0.885499048724-0.6311576618530.1992385704820.089662017705-0.120445351642-0.426593606741-0.5054424532790.2139512701240.470443219084-0.01242838347680.2027503727790.5099741910690.3606116122131.1775121674843.2664572495-72.3676720506-4.7024675909
74.31159090817-2.684869871920.6458281288724.163554218780.2980378388260.999862983467-0.684015208595-1.45813707611-0.5746241248630.4458864227020.9568141862730.08806244635830.192472690887-0.162914243952-0.2346116177060.9207888520560.1422432853060.0568009847350.9009281119020.3659520927010.76502298007940.7343763289-72.3815940289-0.842392441367
82.69258578915-0.9097334385571.302673534041.13028289742-0.2501888824680.694483467174-0.150145813365-0.81946002125-0.7182945613590.2809791383120.02192976345130.6269314951030.279037728478-0.357517548084-0.0980273884110.61155998029-0.00542938435891-0.4557119578671.368307249791.068979422781.050810971721.9667197724-63.8174726477-3.94856716812
91.74446004859-0.3455602886750.3724814264170.5458899972190.1677671010710.1633782662130.424269644408-0.586408144048-1.00071736735-0.1139108643910.1218920181610.2426139030880.99179693642-0.0333598146852-0.5090988078771.04210755129-0.0832084186423-0.6186746798081.099374304020.7661727249312.6643420713425.5864107841-73.3757128767-8.0838761001
101.999854682521.3654243965-8.159347386670.0926172202805-0.5597497165923.3481978653-0.05812937994560.181617549316-0.712268874719-0.09268379784550.1729945749420.8534987580280.898165270819-0.184619116195-0.09385018402471.281280625860.0209154692988-0.6042585339680.7641437504690.219912824341.9244746120128.2746294582-69.7279100355-13.6384214488
113.166398795513.49359628706-0.6256302116473.85972815632-0.6360162618310.5648112948070.005513471408320.121957462719-0.0398075474096-0.0179999658375-0.00358066392404-0.289090058763-0.1339152424150.2374941944970.0001453587574421.15478579091-0.05481013370890.3204857504941.15623545864-0.2212442448990.96355779752932.6245820272-19.3909866885-2.82984603696
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 175 )AA1 - 1751 - 175
22chain 'A' and (resid 176 through 362 )AA176 - 362176 - 362
33chain 'A' and (resid 401 through 401 )AB401
44chain 'A' and (resid 402 through 402 )AC402
55chain 'B' and (resid 1 through 119 )BD1 - 1191 - 119
66chain 'B' and (resid 120 through 174 )BD120 - 174120 - 174
77chain 'B' and (resid 175 through 258 )BD175 - 258175 - 258
88chain 'B' and (resid 259 through 303 )BD259 - 303259 - 303
99chain 'B' and (resid 304 through 362 )BD304 - 362304 - 362
1010chain 'B' and (resid 401 through 401 )BE401
1111chain 'B' and (resid 402 through 402 )BF402

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