4lef

Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site

Method: X-RAY DIFFRACTION D_max: 142.0 Å Quality: GOOD

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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 C； UniProt 1–292	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–292	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–292	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–292	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–292	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–292	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
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–292	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
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–292	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

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 4LEF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BF6 PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI Deposited 1998-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–292（291 aa）	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
1BF6 PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI Deposited 1998-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–292（291 aa）	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

1 other PDB entries and 2 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 1–292； UniProt 1–292 Author chain B； PDBConstruct 1–292； UniProt 1–292 Author chain C； PDBConstruct 1–292； UniProt 1–292 Author chain D； PDBConstruct 1–292； UniProt 1–292 Author chain E； PDBConstruct 1–292； UniProt 1–292 Author chain F； PDBConstruct 1–292； UniProt 1–292 Author chain G； PDBConstruct 1–292； UniProt 1–292 Author chain H； PDBConstruct 1–292； UniProt 1–292

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4lef
Deposition date deposition_date	2013-06-25
Structure title title	Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site
Keywords keywords	PHP fold, HYDROLASE; HYDROLASE
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	46.22 Å
Radius of gyration Rg (electron density) rg_electron	45.78 Å
Forward intensity I(0) i0	1138040000.00
Molecular weight molecular_weight	265910.0 kDa
Excluded volume excluded_volume	326650 Å³
Envelope volume envelope_volume	430500 Å³
Hydration-shell volume shell_volume	77040 Å³
Envelope diameter envelope_diameter	150.4 Å
Shell Rg shell_rg	51.97 Å
Envelope Rg envelope_rg	44.40 Å
Shape Rg shape_rg	45.80 Å
Total Rg total_rg	45.96 Å
Total atoms total_atoms	18537
Residues n_residues	2323
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	142.0 Å
Rg (real space) rg_real	45.94 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.1380e+09
I(0) uncertainty (real space) i0_real_error	2.1870e+07
Rg (reciprocal space) rg_reciprocal	46.22 Å
I(0) (reciprocal space) i0_reciprocal	1138000000.0000
Solution quality estimate total_estimate	0.8804
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.6 Å
Skewness Skewness skewness	0.072
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39810000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.778

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Phosphotriesterase homology protein
Molecular weight formula_weight	32951.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,A,B,E,F,G,H
Atom count atom_count	20380

MSFDPTGYTLAHEHLHIDLSGFKNNVDCRLDQYAFICQEMNDLMTRGVRNVIEMTNRYMGRNAQFMLDVMRETGINVVACTGYYQDAFFPEHVATRSVQELAQEMVDEIEQGIDGTELKAGIIAEIGTSEGKITPLEEKVFIAAALAHNQTGRPISTHTSFSTMGLEQLALLQAHGVDLSRVTVGHCDLKDNLDNILKMIDLGAYVQFDTIGKNSYYPDEKRIAMLHALRDRGLLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRENPSQFFQ

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
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	16

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	31

Entity 4 Entity 4 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1719

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4lefa_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefb_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefc_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefd_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefe_
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.1.9.0 — automated matches

Domain ID domain_id	d4leff_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefg_
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.1.9.0 — automated matches

Domain ID domain_id	d4lefh_
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.1.9.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4lefA00
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	4lefB00
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	4lefC00
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	4lefD00
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	4lefE00
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	4lefF00
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	4lefG00
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	4lefH00
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 (1)

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Unit-cell length a length_a	83.048 Å
Unit-cell length b length_b	100.308 Å
Unit-cell length c length_c	168.037 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.842 Å
Low-resolution limit resolution_low	42.572 Å
R factor r_factor	0.1756
R_work r_work	0.1746
R_free r_free	0.2078

fit	/app/data/saxs_computation/le/4lef/4lef.fit
pddf	/app/data/pr_computation/le/4lef/4lef.pr.out
profile	/app/data/saxs_computation/le/4lef/4lef.dat