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- PDB-1gxq: Crystal structure of the PhoB effector domain -

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Basic information

Entry
Database: PDB / ID: 1gxq
TitleCrystal structure of the PhoB effector domain
ComponentsPHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
KeywordsTRANSCRIPTIONAL ACTIVATOR / HELIX-WINGED-HELIX / SENSORY TRANSDUCTION / PHOSPHORYLATION / DNA BINDING / ACTIVATOR / TWO-COMPONENT SIGNAL TRANSDUCTION
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator activity / regulation of DNA-templated transcription initiation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBlanco, A.G. / Sola, M. / Gomis-Ruth, F.X. / Coll, M.
CitationJournal: Structure / Year: 2002
Title: Tandem DNA Recognition by Two-Component Signal Transduction Transcriptional Activator Phob
Authors: Blanco, A.G. / Sola, M. / Gomis-Ruth, F.X. / Coll, M.
History
DepositionApr 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)12,3581
Polymers12,3581
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.650, 37.290, 30.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

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Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB / PHOB


Mass: 12358.092 Da / Num. of mol.: 1
Fragment: DNA-BINDING AND TRANSACTIVATION DOMAIN, UNP RESIDUES 124-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: PCR-CLONED DOMAIN FROM GENOMIC DNA / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.95 Å3/Da / Density % sol: 68 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMbis-Tris1drop
20.5 M1dropNaCl
311 mg/mlprotein1drop
4100 mMsodium cacodylate1reservoirpH6.5
5200 mMsodium acetate1reservoir
630 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorDate: Dec 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→21.2 Å / Num. obs: 6550 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.1 / % possible all: 71.1
Reflection
*PLUS
Num. measured all: 62124
Reflection shell
*PLUS
% possible obs: 71.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQI

1qqi


Resolution: 2→21 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 -10 %RANDOM
Rwork0.2 ---
obs0.2 6514 100 %-
Displacement parametersBiso mean: 25.54 Å2
Refinement stepCycle: LAST / Resolution: 2→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 66 927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.285

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