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- PDB-1dbw: CRYSTAL STRUCTURE OF FIXJ-N -

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Basic information

Entry
Database: PDB / ID: 1dbw
TitleCRYSTAL STRUCTURE OF FIXJ-N
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
KeywordsTRANSCRIPTION / DOUBLY WOUND FIVE-STRANDED BETA/ALPHA FOLD / NITROGEN FIXATION REGULATION
Function / homology
Function and homology information


nitrogen fixation / DNA-binding transcription activator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein FixJ
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsGouet, P. / Fabry, B. / Guillet, V. / Birck, C. / Mourey, L. / Kahn, D. / Samama, J.P.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Structural transitions in the FixJ receiver domain.
Authors: Gouet, P. / Fabry, B. / Guillet, V. / Birck, C. / Mourey, L. / Kahn, D. / Samama, J.P.
#1: Journal: To be Published
Title: Conformational changes induced by phosphorylation of the FixJ receiver domain
Authors: Birck, C. / Mourey, L. / Gouet, P. / Fabry, B. / Schumacher, J. / Rousseau, P. / Kahn, D. / Samama, J.P.
History
DepositionNov 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
B: TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2903
Polymers27,7602
Non-polymers1,5301
Water2,666148
1
A: TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4102
Polymers13,8801
Non-polymers1,5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ


Theoretical massNumber of molelcules
Total (without water)13,8801
Polymers13,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.700, 42.200, 44.600
Angle α, β, γ (deg.)93.20, 104.50, 101.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ


Mass: 13880.008 Da / Num. of mol.: 2 / Fragment: FIXJ RECEIVER DOMAIN (RESIDUES 1-126) / Mutation: T2Q, A125L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P10958
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal
*PLUS
Density % sol: 30 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 mMTris-HCl1drop
30.1 mMEDTA1drop
41 mMdithiothreitol1drop
540 %(w/v)PEG15001reservoir
620 mMTris-HCl1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONLURE DW3210.93
SYNCHROTRONESRF ID14-420.95
Detector
TypeIDDetectorDate
MARRESEARCH1AREA DETECTORApr 4, 1998
MARRESEARCH2CCDFeb 25, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
20.951
ReflectionResolution: 1.6→30 Å / Num. all: 62615 / Num. obs: 20628 / % possible obs: 73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.123 / % possible all: 20.2
Reflection
*PLUS
Num. measured all: 62615
Reflection shell
*PLUS
% possible obs: 20.2 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→14.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 625584.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1204 5.8 %RANDOM
Rwork0.187 ---
all0.189 28673 --
obs0.187 20600 72.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.5 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å21.03 Å21.33 Å2
2---0.96 Å21.06 Å2
3----1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 19 148 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.511.5
X-RAY DIFFRACTIONc_mcangle_it3.62
X-RAY DIFFRACTIONc_scbond_it3.842
X-RAY DIFFRACTIONc_scangle_it5.62.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 54 5.6 %
Rwork0.232 914 -
obs--20.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3CAM.PARCAM.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.6

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