[English] 日本語
Yorodumi
- PDB-8js6: Dimeric PAS domains of oxygen sensor FixL in complex with cyanide... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8js6
TitleDimeric PAS domains of oxygen sensor FixL in complex with cyanide-bound ferric heme
ComponentsSensor protein FixL
KeywordsTRANSFERASE / heme-binding / PAS / coiled-coil
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / 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 ...: / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Sensor protein FixL
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 2.7 Å
AuthorsKamaya, M. / Koteishi, H. / Sawai, H. / Sugimoto, H. / Shiro, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To be published
Title: Dimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme.
Authors: Koteishi, H. / Sugimoto, H.
#1: Journal: Sci Signal / Year: 2018
Title: Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system.
Authors: Wright, G.S.A. / Saeki, A. / Hikima, T. / Nishizono, Y. / Hisano, T. / Kamaya, M. / Nukina, K. / Nishitani, H. / Nakamura, H. / Yamamoto, M. / Antonyuk, S.V. / Hasnain, S.S. / Shiro, Y. / Sawai, H.
History
DepositionJun 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor protein FixL
B: Sensor protein FixL
C: Sensor protein FixL
D: Sensor protein FixL
E: Sensor protein FixL
F: Sensor protein FixL
G: Sensor protein FixL
H: Sensor protein FixL
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,35945
Polymers306,55210
Non-polymers7,80635
Water1,13563
1
A: Sensor protein FixL
B: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-77 kcal/mol
Surface area26310 Å2
MethodPISA
2
C: Sensor protein FixL
D: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-79 kcal/mol
Surface area26320 Å2
MethodPISA
3
E: Sensor protein FixL
F: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-75 kcal/mol
Surface area27070 Å2
MethodPISA
4
G: Sensor protein FixL
H: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-77 kcal/mol
Surface area26530 Å2
MethodPISA
5
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-77 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.834, 198.733, 266.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein
Sensor protein FixL


Mass: 30655.225 Da / Num. of mol.: 10 / Fragment: oxygen sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: fixL, bll2760 / Plasmid: pE-SUMO Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23222, histidine kinase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5 M Ammonium sulfate, 0.1 M MES, 0.05 M KCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.7382 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7382 Å / Relative weight: 1
ReflectionResolution: 2.7→49.69 Å / Num. obs: 135992 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 15.5 / Num. measured all: 1799377 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.7514.22.4019551167070.5820.6592.491.2100
14.79-49.6912.60.037114779080.9990.0110.03950.497.6

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.3data scaling
SHELX2018/2phasing
PDB_EXTRACT3.27data extraction
XDS20180126data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.68 Å / SU ML: 0.3887 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 + omega-cdl
RfactorNum. reflection% reflection
Rfree0.2472 6822 5.02 %
Rwork0.2186 129092 -
obs0.22 135914 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 135.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19830 0 540 63 20433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007320849
X-RAY DIFFRACTIONf_angle_d1.0728283
X-RAY DIFFRACTIONf_chiral_restr0.05742982
X-RAY DIFFRACTIONf_plane_restr0.00953686
X-RAY DIFFRACTIONf_dihedral_angle_d28.61957624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.38941890.37944303X-RAY DIFFRACTION99.67
2.73-2.760.35292440.34934241X-RAY DIFFRACTION100
2.76-2.80.3332100.32244321X-RAY DIFFRACTION99.98
2.8-2.830.33522430.30454218X-RAY DIFFRACTION99.98
2.83-2.870.24752030.28214276X-RAY DIFFRACTION99.96
2.87-2.910.30382030.28294316X-RAY DIFFRACTION99.96
2.91-2.950.31922330.28624233X-RAY DIFFRACTION100
2.95-2.990.30182140.28224305X-RAY DIFFRACTION99.93
2.99-3.040.27852380.2784278X-RAY DIFFRACTION100
3.04-3.090.34842380.32454238X-RAY DIFFRACTION99.93
3.09-3.140.33792310.34554254X-RAY DIFFRACTION99.96
3.14-3.20.32422460.30994273X-RAY DIFFRACTION100
3.2-3.260.29032350.27874295X-RAY DIFFRACTION99.96
3.26-3.330.26372220.24194285X-RAY DIFFRACTION99.93
3.33-3.40.23922450.21964259X-RAY DIFFRACTION100
3.4-3.480.23642020.21684319X-RAY DIFFRACTION99.98
3.48-3.570.23362390.22134272X-RAY DIFFRACTION100
3.57-3.660.28992510.23454262X-RAY DIFFRACTION99.98
3.66-3.770.26982180.24414292X-RAY DIFFRACTION99.98
3.77-3.890.25682200.21394316X-RAY DIFFRACTION100
3.89-4.030.21072490.20694287X-RAY DIFFRACTION99.98
4.03-4.190.21062090.19534295X-RAY DIFFRACTION100
4.19-4.380.21142320.18364313X-RAY DIFFRACTION99.98
4.39-4.620.20872090.1794335X-RAY DIFFRACTION99.96
4.62-4.90.20472280.17664336X-RAY DIFFRACTION99.87
4.91-5.280.20922370.19274317X-RAY DIFFRACTION99.91
5.28-5.810.29212320.23524331X-RAY DIFFRACTION99.98
5.81-6.650.25342290.22624389X-RAY DIFFRACTION100
6.65-8.370.23932360.2064387X-RAY DIFFRACTION99.98
8.38-49.680.23032370.17964546X-RAY DIFFRACTION99.69

+
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