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- PDB-5xt2: Crystal structures of full-length FixJ from B. japonicum crystall... -

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Basic information

Entry
Database: PDB / ID: 5xt2
TitleCrystal structures of full-length FixJ from B. japonicum crystallized in space group P212121
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 / MOLECULAR REPLACEMENT / Resolution: 2.652 Å
AuthorsNishizono, Y. / Hisano, T. / Shiro, Y. / Sawai, H. / Wright, G.S.A. / Saeki, A. / Hikima, T. / Nakamura, H. / 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 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator FixJ
B: Response regulator FixJ
C: Response regulator FixJ
D: Response regulator FixJ
E: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,96025
Polymers116,7795
Non-polymers1,18020
Water2,936163
1
A: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7948
Polymers23,3561
Non-polymers4397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4263
Polymers23,3561
Non-polymers702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7957
Polymers23,3561
Non-polymers4396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5645
Polymers23,3561
Non-polymers2084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Response regulator FixJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3802
Polymers23,3561
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.722, 137.910, 142.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Response regulator FixJ


Mass: 23355.830 Da / Num. of mol.: 5
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.264 Å3/Da / Density % sol: 62.3 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pentaerythritol ethoxylate, magnesium 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: RAYONIX MX225-HS / Detector: CCD / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 47221 / % possible obs: 99.6 % / Redundancy: 28.2 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.012 / Net I/σ(I): 60.3
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.127 / Mean I/σ(I) obs: 2 / Num. unique obs: 2050 / CC1/2: 0.952 / Rpim(I) all: 0.266 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.652→49.512 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.83 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2485 1995 4.81 %
Rwork0.2062 --
obs0.2083 41518 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.652→49.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7509 0 74 163 7746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137689
X-RAY DIFFRACTIONf_angle_d1.34510358
X-RAY DIFFRACTIONf_dihedral_angle_d6.244713
X-RAY DIFFRACTIONf_chiral_restr0.0611223
X-RAY DIFFRACTIONf_plane_restr0.0081354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6521-2.71840.3616800.26741689X-RAY DIFFRACTION57
2.7184-2.79190.30331030.25122110X-RAY DIFFRACTION70
2.7919-2.87410.34211220.24892495X-RAY DIFFRACTION84
2.8741-2.96680.3051540.25072808X-RAY DIFFRACTION95
2.9668-3.07290.29031460.25133012X-RAY DIFFRACTION100
3.0729-3.19590.32641480.2512990X-RAY DIFFRACTION100
3.1959-3.34130.28151540.23562992X-RAY DIFFRACTION100
3.3413-3.51740.28671530.23032995X-RAY DIFFRACTION100
3.5174-3.73770.25621550.20023029X-RAY DIFFRACTION100
3.7377-4.02620.23881520.18533014X-RAY DIFFRACTION100
4.0262-4.43110.21011490.1663025X-RAY DIFFRACTION100
4.4311-5.07180.18241580.16273071X-RAY DIFFRACTION100
5.0718-6.38770.26741570.21593086X-RAY DIFFRACTION100
6.3877-49.52090.18491640.18663207X-RAY DIFFRACTION99
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)
12.61680.2196-0.95682.4671-0.00543.4408-0.16790.20010.2056-0.02280.0469-0.2662-0.28480.61870.08630.2551-0.08170.03470.33440.02960.163947.036398.022793.4458
22.73453.3899-3.94868.6791-6.13728.02710.0194-0.4974-0.16740.457-0.3816-0.2028-0.1240.53910.33670.3281-0.15940.19550.75070.01910.428958.2952104.551771.8882
32.21760.1165-0.08962.5906-0.92424.8866-0.3178-0.02750.0913-0.04640.12360.7546-0.20540.01790.18340.3262-0.1110.02250.2873-0.04380.545857.9522109.298552.5595
41.317-0.27560.22381.2745-0.21441.3936-0.0499-0.4331-0.41580.65970.0707-0.24230.260.0137-0.04820.91550.1407-0.38470.11770.27-0.04126.341239.679146.2719
52.0656-1.14011.71692.0026-8.45719.47930.11740.59550.1187-0.5367-0.2428-0.0450.24690.33110.13570.92990.1354-0.45040.66260.08660.391216.455133.546968.1684
64.9851-0.8373-0.70275.3495-0.2946.575-0.038-0.3854-0.21750.1157-0.06620.41920.72770.0390.03630.528-0.0433-0.25530.43680.07360.44617.268429.510987.3541
73.97460.22180.70812.7033-0.03892.5962-0.16620.12730.4472-0.59950.12170.8932-0.02790.0660.03270.278-0.0416-0.17590.316-0.07570.598253.442484.575952.2907
87.72466.0807-5.59237.5034-4.17037.5618-0.12590.3209-0.3168-0.4951-0.0736-0.5720.12960.33540.17950.59070.09690.2680.5004-0.11830.270445.726877.111174.682
96.47980.720.20266.1252-0.09555.0968-0.24650.0445-0.51880.04640.02340.51190.4564-0.19160.2130.2280.00240.07610.1781-0.0520.246333.695876.667289.977
103.75150.57620.14391.8899-0.19333.83950.4293-0.17940.5257-0.0076-0.13311.4892-0.5563-0.5496-0.23620.43430.0808-0.05510.3578-0.08460.961815.208654.566687.9854
112.002-7.30816.15446.6278-6.26946.2192-0.0311-0.7627-0.11760.50940.0554-0.43930.22940.2234-0.03530.72590.1731-0.36520.534-0.13120.43866.141961.70864.8416
126.362-0.2319-0.59148.43790.29145.764-0.35-0.07210.03050.0671-0.00580.65810.1361-0.45870.29690.18420.07490.00810.4186-0.09590.3082-6.17861.697250.1287
131.89320.1982-0.1581.7793-0.05210.93540.1298-0.60450.01180.5705-0.1189-0.17440.0063-0.08340.01880.6217-0.2723-0.27020.5075-0.04081.413322.32969.942246.8784
141.6761-0.85861.39970.4406-0.71861.16450.04090.0372-0.4006-0.50750.26761.27360.3281-0.3342-0.30620.6855-0.4044-0.2151.1260.11131.762534.204493.869439.6207
152.27931.4474-1.02181.2777-1.3362.71690.03570.24150.0941-0.14320.19030.47360.0831-0.7537-0.20720.4081-0.0504-0.30470.60480.21151.597342.0144111.472236.918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 204 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 123 )
5X-RAY DIFFRACTION5chain 'B' and (resid 124 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 204 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 123 )
8X-RAY DIFFRACTION8chain 'C' and (resid 124 through 141 )
9X-RAY DIFFRACTION9chain 'C' and (resid 142 through 204 )
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 123 )
11X-RAY DIFFRACTION11chain 'D' and (resid 124 through 141 )
12X-RAY DIFFRACTION12chain 'D' and (resid 142 through 204 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 123 )
14X-RAY DIFFRACTION14chain 'E' and (resid 124 through 141 )
15X-RAY DIFFRACTION15chain 'E' and (resid 142 through 204 )

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