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- PDB-1gxp: PhoB effector domain in complex with pho box DNA. -

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Basic information

Entry
Database: PDB / ID: 1gxp
TitlePhoB effector domain in complex with pho box DNA.
Components
  • 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'
  • 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
  • PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
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 / DNA-binding transcription activator 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
DNA / DNA (> 10) / Phosphate regulon transcriptional regulatory protein PhoB / Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
C: 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
D: 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'
E: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
F: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
G: 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
H: 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)77,6758
Polymers77,6758
Non-polymers00
Water3,243180
1
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
C: 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
D: 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)38,8374
Polymers38,8374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
F: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
G: 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
H: 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)38,8374
Polymers38,8374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.106, 74.106, 289.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN / PHOB


Mass: 12358.092 Da / Num. of mol.: 4
Fragment: DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
Source method: isolated from a genetically manipulated source
Details: BOUND TO DNA, DNA CHAINS C, D, G, H / 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: P08402, UniProt: P0AFJ5*PLUS
#2: DNA chain 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'


Mass: 7120.608 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'


Mass: 7000.536 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.0
31 M1reservoirLiCl
422 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: QUANTUM / Detector: CCD / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→64.6 Å / Num. obs: 29719 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.1 / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 64.6 Å / Num. measured all: 94255
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 76.4 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.324
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2131 7.2 %RANDOM
Rwork0.244 ---
obs0.247 29662 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 1874 0 180 5416
Refinement
*PLUS
% reflection Rfree: 7 % / Rfactor obs: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.469

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