SAXSdb — 1zes

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–125	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–125 Chain C； UniProt 1–125	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

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 1ZES	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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

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 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125 Author chain C； PDBConstruct 1–125； UniProt 1–125

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	1zes
Deposition date deposition_date	2005-04-19
Structure title title	BeF3- activated PhoB receiver domain
Keywords keywords	chey-like fold, response regulator, transcription factor, phob, activated, TRANSCRIPTION ACTIVATOR; TRANSCRIPTION 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	27.54 Å
Radius of gyration Rg (electron density) rg_electron	27.10 Å
Forward intensity I(0) i0	27848800.00
Molecular weight molecular_weight	40651.0 kDa
Excluded volume excluded_volume	50886 Å³
Envelope volume envelope_volume	63069 Å³
Hydration-shell volume shell_volume	21569 Å³
Envelope diameter envelope_diameter	95.4 Å
Shell Rg shell_rg	31.61 Å
Envelope Rg envelope_rg	26.95 Å
Shape Rg shape_rg	27.10 Å
Total Rg total_rg	27.61 Å
Total atoms total_atoms	2850
Residues n_residues	359
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	91.5 Å
Rg (real space) rg_real	27.90 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	2.7850e+07
I(0) uncertainty (real space) i0_real_error	3.9700e+05
Rg (reciprocal space) rg_reciprocal	27.79 Å
I(0) (reciprocal space) i0_reciprocal	27850000.0000
Solution quality estimate total_estimate	0.8089
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.538
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12700000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.670; Smooth: 0.893

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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 phoB
Molecular weight formula_weight	14344.5 kDa
Mutation mutation	P125Q
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3029

MARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRISQ

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 BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1zesa_
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	d1zesb_
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	d1zesc_
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 (3 domains)

Domain ID domain_id	1zesA00
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	1zesB00
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	1zesC00
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 (1)

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Unit-cell length a length_a	77.869 Å
Unit-cell length b length_b	77.869 Å
Unit-cell length c length_c	109.071 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	26.700 Å
R factor r_factor	0.1936
R_work r_work	0.1888
R_free r_free	0.2401

fit	/app/data/saxs_computation/ze/1zes/1zes.fit
pddf	/app/data/pr_computation/ze/1zes/1zes.pr.out
profile	/app/data/saxs_computation/ze/1zes/1zes.dat

BeF3- activated PhoB receiver domain

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