SAXSdb — 1gxp

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN

ESCHERICHIA COLI

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 124–229 Chain B； UniProt 124–229	Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229	;5'-D(GPAPGPCPTPGPTPCPAPTP* APAPAPGPTPTPGPTPCPAPCPGPG)-3' ; × 1 ;5'-D(CPCPCPGPTPGPAPCPAPAP* CPTPTPTPAPTPGPAPCPAPGPCPT)-3' ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50	Resolution 2.50 Å R-free 0.289
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain E； UniProt 124–229 Chain F； UniProt 124–229	Fragment：DNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229	;5'-D(GPAPGPCPTPGPTPCPAPTP* APAPAPGPTPTPGPTPCPAPCPGPG)-3' ; × 1 ;5'-D(CPCPCPGPTPGPAPCPAPAP* CPTPTPTPAPTPGPAPCPAPGPCPT)-3' ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50	Resolution 2.50 Å R-free 0.289

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 1GXP	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
1QQI SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI Deposited 1999-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 126–229（104 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	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
1ZES BeF3- activated PhoB receiver domain Deposited 2005-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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 5 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 1–106； UniProt 124–229 Author chain B； PDBConstruct 1–106； UniProt 124–229 Author chain E； PDBConstruct 1–106； UniProt 124–229 Author chain F； PDBConstruct 1–106； UniProt 124–229

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gxp
Deposition date deposition_date	2002-04-08
Structure title title	PhoB effector domain in complex with pho box DNA.
Keywords keywords	;TRANSCRIPTIONAL ACTIVATOR, HELIX-WINGED-HELIX, SENSORY TRANSDUCTION, PHOSPHORYLATION, DNA BINDING, ACTIVATOR, TWO- COMPONENT SIGNAL TRANSDUCTION ;; TRANSCRIPTIONAL ACTIVATOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.61 Å
Radius of gyration Rg (electron density) rg_electron	32.78 Å
Forward intensity I(0) i0	144211000.00
Molecular weight molecular_weight	76034.0 kDa
Excluded volume excluded_volume	86569 Å³
Envelope volume envelope_volume	123240 Å³
Hydration-shell volume shell_volume	33155 Å³
Envelope diameter envelope_diameter	122.2 Å
Shell Rg shell_rg	37.03 Å
Envelope Rg envelope_rg	32.87 Å
Shape Rg shape_rg	32.73 Å
Total Rg total_rg	33.19 Å
Total atoms total_atoms	5236
Residues n_residues	500
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.2 Å
Rg (real space) rg_real	33.84 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	1.4420e+08
I(0) uncertainty (real space) i0_real_error	2.4610e+06
Rg (reciprocal space) rg_reciprocal	33.70 Å
I(0) (reciprocal space) i0_reciprocal	144200000.0000
Solution quality estimate total_estimate	0.8426
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.558
Kurtosis Kurtosis kurtosis	-0.040
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7695000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.754

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
Molecular weight formula_weight	12358.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	5416

SPMAVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(GPAPGPCPTPGPTPCPAPTP* APAPAPGPTPTPGPTPCPAPCPGPG)-3' ;
Molecular weight formula_weight	7120.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G

GAGCTGTCATAAAGTTGTCACGG

Entity 3 Entity 3 polymer

Description description	;5'-D(CPCPCPGPTPGPAPCPAPAP* CPTPTPTPAPTPGPAPCPAPGPCPT)-3' ;
Molecular weight formula_weight	7000.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

CCCGTGACAACTTTATGACAGCT

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1gxpa_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.1 — PhoB-like

Domain ID domain_id	d1gxpb_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.1 — PhoB-like

Domain ID domain_id	d1gxpe_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.1 — PhoB-like

Domain ID domain_id	d1gxpf_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.1 — PhoB-like

CATH v4.4 (4 domains)

Domain ID domain_id	1gxpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1gxpB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1gxpE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1gxpF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	74.106 Å
Unit-cell length b length_b	74.106 Å
Unit-cell length c length_c	289.682 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2470
R_work r_work	0.2440
R_free r_free	0.2890

fit	/app/data/saxs_computation/gx/1gxp/1gxp.fit
pddf	/app/data/pr_computation/gx/1gxp/1gxp.pr.out
profile	/app/data/saxs_computation/gx/1gxp/1gxp.dat

PhoB effector domain in complex with pho box DNA.

1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)