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1qqi

SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI

Method: SOLUTION NMR Dmax: 50.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB

Escherichia coli

UniProt P08402

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 126–229 Fragment：C-TERMINAL DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；300 K；Ionic strength (raw mmCIF value) NACL 500mM；Pressure AMBIENT NMR sample composition：1-2MM PROTEIN U-15N,13C; 50MM PHOSPHATE BUFFER, 500MM NACL NMR sample composition：1-2MM PROTEIN U-15N; 50MM PHOSPHATE BUFFER, 500MM NACL NMR sample composition：1-2MM PROTEIN ; 50MM PHOSPHATE BUFFER, 500MM NACL Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1QQI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B00 PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI Deposited 1998-11-15 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–127（127 aa） Fragment：RECEIVER DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.88 Å R-free 0.280
1B00 PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI Deposited 1998-11-15 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–127（127 aa） Fragment：RECEIVER DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.88 Å R-free 0.280
1GXP PhoB effector domain in complex with pho box DNA. Deposited 2002-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 124–229（106 aa） Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
Chain B 124–229（106 aa） Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.50 Å R-free 0.289
1GXP PhoB effector domain in complex with pho box DNA. Deposited 2002-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain E 124–229（106 aa） Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
Chain F 124–229（106 aa） Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.50 Å R-free 0.289
1ZES BeF3- activated PhoB receiver domain Deposited 2005-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–125（125 aa） Fragment：N-terminal domain (residues 1-125)
Mutation：P125Q MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；sodium thiocyanate, Peg3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.240
1ZES BeF3- activated PhoB receiver domain Deposited 2005-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–125（125 aa） Fragment：N-terminal domain (residues 1-125)
Chain C 1–125（125 aa） Fragment：N-terminal domain (residues 1-125)
Mutation：P125Q Mutation：P125Q MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；sodium thiocyanate, Peg3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.240

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHOB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–104； UniProt 126–229

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1qqi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qqi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1qqi
Deposition date deposition_date1999-06-07
Structure title titleSOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI
Keywords keywordsWINGED HELIX-TURN-HELIX, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.88 Å
Radius of gyration Rg (electron density) rg_electron13.39 Å
Forward intensity I(0) i03228620.00
Molecular weight molecular_weight12153.0 kDa
Excluded volume excluded_volume15059 ų
Envelope volume envelope_volume17343 ų
Hydration-shell volume shell_volume11114 ų
Envelope diameter envelope_diameter47.4 Å
Shell Rg shell_rg18.99 Å
Envelope Rg envelope_rg13.88 Å
Shape Rg shape_rg13.36 Å
Total Rg total_rg14.68 Å
Total atoms total_atoms1691
Residues n_residues104
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.1 Å
Rg (real space) rg_real14.79 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real3.2290e+06
I(0) uncertainty (real space) i0_real_error3.6260e+04
Rg (reciprocal space) rg_reciprocal14.80 Å
I(0) (reciprocal space) i0_reciprocal3229000.0000
Solution quality estimate total_estimate0.8700
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.8 Å
Skewness Skewness skewness0.195
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha689000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1qqia_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family familya.4.6.1 — PhoB-like

CATH v4.4 (1 domains)

Domain ID domain_id1qqiA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)