SAXSdb — 1b00

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

PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–127	Fragment：RECEIVER DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 1.88 Å R-free 0.280
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–127	Fragment：RECEIVER DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 1.88 Å R-free 0.280

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 1B00	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GXP PhoB effector domain in complex with pho box DNA. Deposited 2002-04-08	Different construct Different mutation/modification Different oligomeric state 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 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
1QQI SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI Deposited 1999-06-07	Different construct 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 1–127； UniProt 1–127 Author chain B； PDBConstruct 1–127； UniProt 1–127

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	1b00
Deposition date deposition_date	1998-11-15
Structure title title	PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI
Keywords keywords	TRANSCRIPTION FACTOR, PHOSPHATE REGULATION, ACTIVATION OF THE PHO REGULON, ALPHA/BETA DOUBLY WOUND FOLD, GENE REGULATION; GENE REGULATION
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	21.63 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	13773000.00
Molecular weight molecular_weight	27916.0 kDa
Excluded volume excluded_volume	35016 Å³
Envelope volume envelope_volume	41599 Å³
Hydration-shell volume shell_volume	17680 Å³
Envelope diameter envelope_diameter	73.1 Å
Shell Rg shell_rg	26.17 Å
Envelope Rg envelope_rg	20.95 Å
Shape Rg shape_rg	20.60 Å
Total Rg total_rg	21.39 Å
Total atoms total_atoms	1960
Residues n_residues	244
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	75.0 Å
Rg (real space) rg_real	21.74 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.3770e+07
I(0) uncertainty (real space) i0_real_error	2.1710e+05
Rg (reciprocal space) rg_reciprocal	21.72 Å
I(0) (reciprocal space) i0_reciprocal	13770000.0000
Solution quality estimate total_estimate	0.8366
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.489
Kurtosis Kurtosis kurtosis	-0.243
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5337000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.858; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b00a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

Domain ID domain_id	d1b00b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

CATH v4.4 (2 domains)

Domain ID domain_id	1b00A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1b00B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (2)

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Unit-cell length a length_a	34.110 Å
Unit-cell length b length_b	60.420 Å
Unit-cell length c length_c	119.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2100
R_free r_free	0.2800

Description description	PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
Molecular weight formula_weight	14515.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2091

PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI

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

PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	131

fit	/app/data/saxs_computation/b0/1b00/1b00.fit
pddf	/app/data/pr_computation/b0/1b00/1b00.pr.out
profile	/app/data/saxs_computation/b0/1b00/1b00.dat