SAXSdb — 1bf6

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

PHOSPHOTRIESTERASE HOMOLOGY 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–292	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.241
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–292	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.241

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 1BF6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 5 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208
4LEF Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–292（292 aa）	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M ammonium phosphate, 50mM Hepes, 10% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.84 Å R-free 0.208

1 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–291； UniProt 2–292 Author chain B； PDBConstruct 1–291； UniProt 2–292

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	1bf6
Deposition date deposition_date	1998-05-27
Structure title title	PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI
Keywords keywords	PHOSPHOTRIESTERASE, HYPOTHETICAL PROTEIN; PHOSPHOTRIESTERASE
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	30.48 Å
Radius of gyration Rg (electron density) rg_electron	29.84 Å
Forward intensity I(0) i0	74843900.00
Molecular weight molecular_weight	66191.0 kDa
Excluded volume excluded_volume	81805 Å³
Envelope volume envelope_volume	96122 Å³
Hydration-shell volume shell_volume	27675 Å³
Envelope diameter envelope_diameter	102.5 Å
Shell Rg shell_rg	35.74 Å
Envelope Rg envelope_rg	29.85 Å
Shape Rg shape_rg	29.86 Å
Total Rg total_rg	30.25 Å
Total atoms total_atoms	4623
Residues n_residues	582
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	98.4 Å
Rg (real space) rg_real	30.69 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	7.4840e+07
I(0) uncertainty (real space) i0_real_error	1.1180e+06
Rg (reciprocal space) rg_reciprocal	30.61 Å
I(0) (reciprocal space) i0_reciprocal	74840000.0000
Solution quality estimate total_estimate	0.8222
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.746
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	59250000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.725; Smooth: 0.898

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
Molecular weight formula_weight	32820.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4911

SFDPTGYTLAHEHLHIDLSGFKNNVDCRLDQYAFICQEMNDLMTRGVRNVIEMTNRYMGRNAQFMLDVMRETGINVVACTGYYQDAFFPEHVATRSVQELAQEMVDEIEQGIDGTELKAGIIAEIGTSEGKITPLEEKVFIAAALAHNQTGRPISTHTSFSTMGLEQLALLQAHGVDLSRVTVGHCDLKDNLDNILKMIDLGAYVQFDTIGKNSYYPDEKRIAMLHALRDRGLLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRENPSQFFQ

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bf6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

Domain ID domain_id	d1bf6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1bf6A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1bf6B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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8. Citations (2)

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Unit-cell length a length_a	42.070 Å
Unit-cell length b length_b	80.800 Å
Unit-cell length c length_c	98.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2410

fit	/app/data/saxs_computation/bf/1bf6/1bf6.fit
pddf	/app/data/pr_computation/bf/1bf6/1bf6.pr.out
profile	/app/data/saxs_computation/bf/1bf6/1bf6.dat

PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI