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- PDB-8a7f: Crystal structure of a chimeric LOV-Histidine kinase SB2F1-I66R m... -

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Basic information

Entry
Database: PDB / ID: 8a7f
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1-I66R mutant (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 / I66R mutant
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsBatra-Safferling, R. / Arinkin, V. / Granzin, J.
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 (asymmetrical variant, trigonal form with long c axis)
Authors: Batra-Safferling, R. / Arinkin, V. / Granzin, J.
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)87,8156
Polymers85,8882
Non-polymers1,9274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-85 kcal/mol
Surface area35410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.530, 138.530, 96.894
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_1(chain "B" and (resid 0 through 362 or resid 401 through 402))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISLEUA1 - 363
d_12ens_1ATPATPB
d_13ens_1FMNFMNC
d_21ens_1HISLEUD3 - 365
d_22ens_1ATPATPE
d_23ens_1FMNFMNF

NCS oper: (Code: givenMatrix: (-0.497919523024, -0.867135245602, 0.0123537211896), (-0.866711323187, 0.497085724435, -0.0414398940832), (0.0297931342866, -0.0313408423346, -0.99906462291)Vector: -2. ...NCS oper: (Code: given
Matrix: (-0.497919523024, -0.867135245602, 0.0123537211896), (-0.866711323187, 0.497085724435, -0.0414398940832), (0.0297931342866, -0.0313408423346, -0.99906462291)
Vector: -2.00597214965, -2.24951605607, -13.5521427888)

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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(DE3) (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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / 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: 3.13 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 9% PEG8K, 0.1M Na-Citrate, 0.2M NaCl, 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 PILATUS3 6M / Detector: PIXEL / Date: Jun 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: 2.71→45.345 Å / Num. obs: 16593 / % possible obs: 56.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 86.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 13.4
Reflection shellResolution: 2.71→2.926 Å / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 831 / CC1/2: 0.403 / Rpim(I) all: 0.555 / Rrim(I) all: 1.216

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A6X

8a6x


Resolution: 2.71→45.34 Å / SU ML: 0.2889 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.5501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1000 6.03 %
Rwork0.2283 15582 -
obs0.2296 16582 56.08 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.48 Å2
Refinement stepCycle: LAST / Resolution: 2.71→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5662 0 124 0 5786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425874
X-RAY DIFFRACTIONf_angle_d0.76067961
X-RAY DIFFRACTIONf_chiral_restr0.0515887
X-RAY DIFFRACTIONf_plane_restr0.00571054
X-RAY DIFFRACTIONf_dihedral_angle_d15.76922251
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.5956549879 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-3.10.41091350.38251839X-RAY DIFFRACTION20.33
3.1-3.90.30843080.29795008X-RAY DIFFRACTION54.21
3.9-45.340.22895570.20678735X-RAY DIFFRACTION92.49
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)
10.332295650663-1.951676249260.5824572335561.499160781590.484197939658-1.594927203690.07918329840730.1656887465260.3208384064790.3278811343750.1571011980770.282168668036-0.613533391736-0.446373430098-0.1322884291851.258363824140.3828745671970.2690217411560.5633914231220.08816156324120.893473297836-19.368051808243.0696413721-12.9136725704
21.25438183686-0.345263713770.9686851519522.43851246936-0.01244504993390.7068448114310.5329482054140.506035950593-1.1258495131-0.87270823452-0.3186046423170.9413597280310.9950356217660.18973983191-0.2523015929871.989586237580.4736601499230.179663683851.01152591928-0.08741793626521.7086687395-50.687728662359.4177494944-15.3836757515
31.27637826412-0.671287943094-1.022909268932.98591522118-2.217006530013.69995486017-0.3027936109070.902312151527-1.93285284364-0.782627366823-0.05110400977020.09956762522291.13450104109-0.1325900282030.2871301933962.425681206360.5118970717220.06192022093080.944146252917-0.3497863530471.65043553153-52.717228495256.9164354189-6.80415118327
45.79118543328-3.924206918932.059032215224.38565296425-0.2741751307667.56634540937-0.109775889924-0.0372105880730.441031581538-0.430566155650.22454828304-0.280230549875-0.5237275733620.0319671304516-0.09376326531431.56455356366-0.09300103441810.377920135372-0.314989361114-0.5820239823290.529665075114-4.9948860950936.3836485697-12.4473769379
53.15671695850.0612415541107-0.1815758356183.09607789248-1.147252741133.562145697660.37791145913-0.0594829961630.1420213842660.202490910619-0.08276812313360.606886166958-1.05592134865-1.52495603872-0.1474051041010.618707206590.3549222131240.0641578592780.344748918911-0.08087443038090.407170052239-23.650750048220.2256542758-2.41803570683
61.36050137737-3.941061435970.1303130725688.55090269885-0.46545082603-0.320024720872-0.6424349292330.192826799153-0.337736989236-0.199420422044-0.0706318009684-0.5064408296291.14154464830.7084128969370.3406635854721.557245884851.284943287890.762143876869-0.156155977561-0.2551461900020.949735360839-41.12029159272.7168435544-3.19466155424
72.69725225441-1.667072523850.773588545972.098447465710.8913305723031.03063899608-0.48867657549-0.2273186430890.1288483855961.076756180650.608540224133-1.122683883820.7993105606361.10769922348-0.2416578094821.81667168020.7156176882210.1490032525661.513479852820.1230243878961.49665125543-29.203462713871.756354877-1.59460476449
82.989359957221.280824615072.592813644262.62792435114-0.3978551494523.337735317210.268680830497-0.537379631519-0.9802895389370.960175984204-0.0752118696867-1.663932813660.6120727924050.903060594491-0.1984101663691.827308610780.609364401742-0.1555503109091.384379876040.5718667616171.25553417603-26.114358733270.9418124169-10.6343793762
92.65570638277-1.30610289202-0.6457840874541.691096392880.6241498220640.245839544895-0.100536951103-0.794530627479-0.01895887955590.08125449373940.08400377930530.612180705409-0.274525115958-0.7539623680710.06576370260670.3983609645280.535045738799-0.1663269440131.291565171530.09326962428880.621982927571-30.60021111920.4639077995-2.36703971467
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 176 )AA0 - 1761 - 177
22chain 'A' and (resid 177 through 362 )AA177 - 362178 - 363
33chain 'A' and (resid 401 through 401 )AB401
44chain 'A' and (resid 402 through 402 )AC402
55chain 'B' and (resid -2 through 119 )BD-2 - 1191 - 122
66chain 'B' and (resid 120 through 174 )BD120 - 174123 - 177
77chain 'B' and (resid 175 through 362 )BD175 - 362178 - 365
88chain 'B' and (resid 401 through 401 )BE401
99chain 'B' and (resid 402 through 402 )BF402

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