[English] 日本語
Yorodumi
- PDB-8a6x: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a6x
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1 (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 / 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: 2.45 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 (asymmetrical variant, trigonal form with long c axis)
Authors: Arinkin, V. / Granzin, J. / Batra-Safferling, R.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)88,6656
Polymers86,7382
Non-polymers1,9274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-79 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.794, 138.794, 96.084
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_1(chain "A" and (resid 0 through 153 or resid 155 through 363 or resid 402 through 500))
d_2ens_1(chain "B" and (resid 0 through 153 or resid 155 through 363 or resid 402 through 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISALAA1 - 154
d_12ens_1GLUPROA156 - 364
d_13ens_1ATPATPB
d_14ens_1FMNFMNC
d_21ens_1HISALAD3 - 156
d_22ens_1GLUPROD158 - 366
d_23ens_1ATPATPE
d_24ens_1FMNFMNF

NCS oper: (Code: givenMatrix: (0.997769000525, 5.39269538263E-5, 0.0667609068541), (-0.000896374319881, -0.999898711196, 0.0142043606889), (0.0667549107196, -0.0142325135301, -0.997667889357)Vector: - ...NCS oper: (Code: given
Matrix: (0.997769000525, 5.39269538263E-5, 0.0667609068541), (-0.000896374319881, -0.999898711196, 0.0142043606889), (0.0667549107196, -0.0142325135301, -0.997667889357)
Vector: -1.65793891575, -4.9784628894, 12.024710424)

-
Components

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


Mass: 43368.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: De Novo Protein, chimeric, engineered; His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; UNP:Q88JB0 (belongs to): 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120 PDB-file); UNP:P23222 (belongs to): ...Details: De Novo Protein, chimeric, engineered; His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; UNP:Q88JB0 (belongs to): 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120 PDB-file); UNP:P23222 (belongs to):141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368 PDB-file); UNP:Q88JB0 (UNP-numbering) 1-(MSE)INA...QRDVT-120; UNP:P23222 (UNP-numbering) 258 to C-Term; All Met are exchanged for SeMet. 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.: 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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG8K, 0.1M Citrate, 0.2M NaCl, 0.1M Ammonium Trifluoroacetate, 1mM ATP, 2mM MgCl2

-
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.45→45.43 Å / Num. obs: 27082 / % possible obs: 68.7 % / Redundancy: 20.1 % / Biso Wilson estimate: 77.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.028 / Rrim(I) all: 0.125 / Net I/σ(I): 20.2
Reflection shellResolution: 2.452→2.6 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1369 / CC1/2: 0.58 / Rpim(I) all: 0.543 / % possible all: 21.9

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.45→45.43 Å / SU ML: 0.4148 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 36.6228
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 (27081 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 (27081 reflections). However, separating the reflections on F(+) and F(-), the Phenix program gives a number of 52123 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
Rfree0.2667 1385 5.12 %
Rwork0.2259 49455 -
obs0.2279 27081 68.66 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.96 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 124 0 5804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785903
X-RAY DIFFRACTIONf_angle_d1.17188007
X-RAY DIFFRACTIONf_chiral_restr0.0636894
X-RAY DIFFRACTIONf_plane_restr0.00581060
X-RAY DIFFRACTIONf_dihedral_angle_d15.6512259
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.55550295225 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.540.6683860.62941161X-RAY DIFFRACTION16.47
2.54-2.640.52531520.48812381X-RAY DIFFRACTION33.33
2.64-2.760.43051640.36413062X-RAY DIFFRACTION42.51
2.76-2.910.362520.33193912X-RAY DIFFRACTION55.05
2.91-3.090.33882440.32244857X-RAY DIFFRACTION67.1
3.09-3.330.32372920.30985664X-RAY DIFFRACTION78.88
3.33-3.660.29254240.25346693X-RAY DIFFRACTION93.68
3.66-4.190.2733480.21917245X-RAY DIFFRACTION100
4.19-5.280.20643230.1827266X-RAY DIFFRACTION100
5.28-45.430.23363830.19167214X-RAY DIFFRACTION99.86
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)
15.13020882324-1.21191673757-0.4481682572254.874185285772.686756315853.894077947180.1652602921480.01442347397550.653494377406-0.383053449050.46396040088-0.404681880208-0.5872013636470.855613954088-0.5132044578470.326501969832-0.1937018732630.1654667182860.460951274221-0.1120167511330.37229425301330.2945774447.8225628959711.840084178
29.22998367493-1.23692852748-1.26660165615-0.9552019736760.4135169854610.295746836627-0.094280849807-0.6152049482420.366082598615-0.0248615682376-0.403306553670.424548974214-0.000150809346064-0.950986828790.4419930751630.402685311148-0.01887034985980.007553819264781.44484289149-0.2305772778971.1385711216884.7446279156-4.5306172954814.0202499072
33.594679341131.294138837011.075657571081.17703539119-0.0508978501691.604959883490.418326578503-1.67038053461-0.5315598497010.365601934549-0.4686431174440.6151911342250.447815358572-1.25756746510.06134357904170.705621818674-0.2139287791010.1977657115741.85477390119-0.07420379774451.4444317991977.1473356701-15.324616563215.4729298247
42.006501818211.99858189604-1.134133260642.000620590783.940350469445.39277937349-0.306153767263-0.771192526792-0.9927211196930.3962643731470.1401406076372.321470607160.501072512732-1.381040927430.07792284001530.742931657286-0.4483949514140.07093857105941.92690916249-0.305273309181.3278836183676.0411790396-18.4259564086.79507861695
52.83185319709-2.104050446623.411025817552.08422656392-2.624285638184.147235802370.760534210809-0.7589399599331.84203530330.723952062785-0.543004755962-0.296158182875-0.4347522899090.665675416909-0.04586345149010.565964396639-0.3181581492860.2627027414680.844629836715-0.3008045629340.7764291741134.437185779213.314474255112.0602976062
63.400742787940.2671362181241.782937983945.733016375012.498567384637.160260599480.343010550880.249728091652-0.696530375066-0.2618757325480.23031714243-0.4430388711430.3211740444921.50012587731-0.4518759086130.1960741332310.02184900017660.08289037447910.611489236959-0.1290877589420.4565734419729.2381752979-10.91672129072.07810374434
79.179756463342.203367381141.19815930194-0.8822525887370.3940476027961.064400752180.0867773550490.02653040924690.5453115189010.226648402814-0.5075801297920.3474541829530.17045066572-0.9453494997940.3464127797270.431121219622-0.1113975548520.1518391176771.32070450609-0.1530203125181.4109407435784.4071788112-0.3569034444943.71011525648
84.8983228127-1.193309193490.01341883165791.019401706380.1780329045941.689968492790.2373537074551.442079912910.402877098688-0.248920632985-0.6092487166430.413593676493-0.230627642466-1.034654096680.340466532610.5715785724040.0193588535597-0.02960230636581.4252691404-0.1381795047460.86255417926179.87962309082.521314689870.576572746023
98.373144240860.735729439652.789001289978.5055401389-2.493762901335.83467016124-1.025532693030.08907250821591.73206887919-0.3656523132160.621921357298-0.854411461824-1.119027776360.2191675769450.3602949343870.963601851413-0.0164036445928-0.03940492935951.19697444371-0.230776317491.5615484879172.001023229616.87111143813.47483357215
107.78833597049-9.93805627405-0.5027735255581.9998078988-1.317737743982.00963380180.2786787532491.195420401830.6591149112880.04871539983921.655229654281.17172518466-0.0517804193394-1.42639864743-1.716414186040.8477486127790.440363678564-0.3172079579341.70823749974-0.3540506162891.5481626222974.063758383712.147913387610.9378599025
116.59658516465-3.571846483872.430832526724.68249984785-1.715449754074.85720220156-0.0852618301683-0.0653524474972-1.08190663903-0.6014588512310.745841746235-1.434317242270.7165718938891.31076512015-0.288249878250.4115153974790.2108702730390.08893266193031.20907800238-0.3032369228690.68757896405532.8422363961-16.99561846291.97112865934
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 119 )AA0 - 1191 - 120
22chain 'A' and (resid 120 through 175 )AA120 - 175121 - 176
33chain 'A' and (resid 176 through 363 )AA176 - 363177 - 364
44chain 'A' and (resid 401 through 401 )AB401
55chain 'A' and (resid 402 through 402 )AC402
66chain 'B' and (resid -2 through 119 )BD-2 - 1191 - 122
77chain 'B' and (resid 120 through 175 )BD120 - 175123 - 178
88chain 'B' and (resid 176 through 274 )BD176 - 274179 - 277
99chain 'B' and (resid 275 through 365 )BD275 - 365278 - 368
1010chain 'B' and (resid 401 through 401 )BE401
1111chain 'B' and (resid 402 through 402 )BF402

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more