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- PDB-1dcm: STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (... -

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Basic information

Entry
Database: PDB / ID: 1dcm
TitleSTRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A)
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: 3 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: Structure / Year: 1999
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 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)27,7843
Polymers27,7602
Non-polymers241
Water21612
1
A: 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
2
B: TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9042
Polymers13,8801
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.600, 34.800, 66.900
Angle α, β, γ (deg.)90.00, 119.40, 90.00
Int Tables number5
Space group name H-MC121
Detailsunphosphorylated FixJN is a monomeric protein

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details15P IS AN N=6 FRAGMENT OF POLYETHYLENE GLYCOL 1500 (N=34). THE REST OF THE MOLECULE WAS NOT VISIBLE ...15P IS AN N=6 FRAGMENT OF POLYETHYLENE GLYCOL 1500 (N=34). THE REST OF THE MOLECULE WAS NOT VISIBLE IN THE ELECTRON DENSITY.

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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: 2 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG1500, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
pH: 7
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
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 14984 / Num. obs: 4760 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.14 / Num. unique all: 461 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 3 Å / Num. measured all: 14984

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 1DBW

1dbw


Resolution: 3→14.92 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 979414.04 / 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
Rfree0.335 515 11 %RANDOM
Rwork0.248 ---
all0.258 4796 --
obs0.248 4663 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.7 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.53 Å20 Å25.55 Å2
2--6.99 Å20 Å2
3----1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 3→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 13 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 89 11.4 %
Rwork0.317 692 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ID14FIT
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 11 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.424 / Rfactor Rwork: 0.317

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