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- PDB-5xso: Crystal structure of full-length FixJ from B. japonicum crystalli... -

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Basic information

Entry
Database: PDB / ID: 5xso
TitleCrystal structure of full-length FixJ from B. japonicum crystallized in space group C2221
ComponentsResponse regulator FixJ
KeywordsDNA BINDING PROTEIN / Response Regulater / FixJ/NarL Family / Full-length / unphosphorylated monomeric state
Function / homology
Function and homology information


Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.778 Å
AuthorsNishizono, Y. / Hisano, T. / Sawai, H. / Shiro, Y. / Nakamura, H. / Wright, G.S.A. / Saeki, A. / Hikima, T. / Yamamoto, M. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: 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 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,00011
Polymers23,3561
Non-polymers64510
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint0 kcal/mol
Surface area11140 Å2
Unit cell
Length a, b, c (Å)70.849, 79.335, 120.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Response regulator FixJ


Mass: 23355.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: fixJ, AF336_29235 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M9B7W0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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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: 3.61 Å3/Da / Density % sol: 65.96 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, PEG 1000, sodium formate, glycerol, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 53635 / % possible obs: 99.5 % / Redundancy: 14.3 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 45.8
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1502 / CC1/2: 0.836 / Rpim(I) all: 0.262 / Rsym value: 0.832 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementResolution: 1.778→39.674 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2044 3397 6.33 %
Rwork0.1707 --
obs0.1729 53635 85.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.778→39.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 42 257 1826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161627
X-RAY DIFFRACTIONf_angle_d1.2682187
X-RAY DIFFRACTIONf_dihedral_angle_d8.0111366
X-RAY DIFFRACTIONf_chiral_restr0.088251
X-RAY DIFFRACTIONf_plane_restr0.008284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7783-1.80370.3131560.2764837X-RAY DIFFRACTION34
1.8037-1.83070.3002710.24751072X-RAY DIFFRACTION43
1.8307-1.85930.2795790.22111198X-RAY DIFFRACTION49
1.8593-1.88980.22271040.22191404X-RAY DIFFRACTION57
1.8898-1.92230.21091010.22351533X-RAY DIFFRACTION63
1.9223-1.95730.21441150.20571739X-RAY DIFFRACTION70
1.9573-1.99490.22491200.19371813X-RAY DIFFRACTION75
1.9949-2.03570.2211370.18642006X-RAY DIFFRACTION81
2.0357-2.07990.20841410.18422103X-RAY DIFFRACTION87
2.0799-2.12830.19961510.1852294X-RAY DIFFRACTION93
2.1283-2.18150.22731610.18112363X-RAY DIFFRACTION96
2.1815-2.24050.22821650.17252436X-RAY DIFFRACTION99
2.2405-2.30640.17031680.17932458X-RAY DIFFRACTION100
2.3064-2.38090.20441620.16532418X-RAY DIFFRACTION100
2.3809-2.46590.19811710.16882481X-RAY DIFFRACTION100
2.4659-2.56470.17971700.17282431X-RAY DIFFRACTION100
2.5647-2.68140.20631660.16762475X-RAY DIFFRACTION100
2.6814-2.82270.18591670.1742464X-RAY DIFFRACTION100
2.8227-2.99950.2021660.16512432X-RAY DIFFRACTION100
2.9995-3.2310.21981670.16952448X-RAY DIFFRACTION100
3.231-3.55590.22581600.1612493X-RAY DIFFRACTION100
3.5559-4.070.18591660.14792434X-RAY DIFFRACTION100
4.07-5.12610.17261690.13832451X-RAY DIFFRACTION100
5.1261-39.68370.22951640.18412455X-RAY DIFFRACTION100
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)
12.12271.4366-0.04213.50270.5163.5890.0809-0.4348-0.52250.03810.3964-0.1420.02310.6198-0.29160.1468-0.0874-0.0880.24030.12870.268210.019412.156413.2311
22.5569-1.5022.57448.2394-6.73216.2987-0.22070.76030.3479-0.6542-0.042-0.0461-0.30250.09270.17930.68250.1540.10940.41430.17110.07717.93036.236639.2738
33.50740.1791-0.39133.98320.5442.00230.05740.29630.0103-0.6438-0.39160.34720.039-0.04060.23110.14760.0689-0.04490.1211-0.05030.083712.0027-3.713251.5099
42.0004-4.55195.96862.43780.12799.8815-0.04620.43160.8722-0.0006-0.04430.2106-1.37340.20870.09420.80030.0637-0.07120.58140.2030.371610.730816.606430.6599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 128 )

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