SAXSdb — 1dkl

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

PHYTASE

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 23–432	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：SMALL TUBES；pH 4.5；273 K；SODIUM ACETATE, pH 4.5, SMALL TUBES, temperature 273K	Resolution 2.30 Å R-free 0.202
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 23–432	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：SMALL TUBES；pH 4.5；273 K；SODIUM ACETATE, pH 4.5, SMALL TUBES, temperature 273K	Resolution 2.30 Å R-free 0.202

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 1DKL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DKM CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE Deposited 1999-12-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：A116T	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.266
1DKN CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 5.0 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE Deposited 1999-12-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：A116T	HG MERCURY (II) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.268
1DKO CRYSTAL STRUCTURE OF TUNGSTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH TUNGSTATE BOUND AT THE ACTIVE SITE AND WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE Deposited 1999-12-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：A116T	HG MERCURY (II) ION × 4 WO4 TUNGSTATE(VI)ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, SODIUM TUNGSTATE, pH 6.60, VAPOR DIFFUSION, SITTING DROP, temperature 298.00K	Resolution 2.38 Å R-free 0.232
1DKP CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE Deposited 1999-12-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：A116T, H17A	HG MERCURY (II) ION × 4 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.28 Å R-free 0.227
1DKQ CRYSTAL STRUCTURE OF PHYTATE COMPLEX ESCHERICHIA COLI PHYTASE AT PH 5.0. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE Deposited 1999-12-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：A116T, H17A	HG MERCURY (II) ION × 4 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.05 Å R-free 0.257
4TSR The Complex Structure of Mutant Phytase with IHS Deposited 2014-06-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–432（410 aa）	Mutation：V89T and S206A	NI NICKEL (II) ION × 4 IHS D-MYO-INOSITOL-HEXASULPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.01 M NiCl2, 0.1 M HEPES, 20% PEG 3350 and 2% PEG 8000	Resolution 2.07 Å R-free 0.218

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–410； UniProt 23–432 Author chain B； PDBConstruct 1–410； UniProt 23–432

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	1dkl
Deposition date deposition_date	1999-12-08
Structure title title	CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)
Keywords keywords	HISTIDINE ACID PHOSPHATASE 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	33.07 Å
Radius of gyration Rg (electron density) rg_electron	32.71 Å
Forward intensity I(0) i0	122331000.00
Molecular weight molecular_weight	87645.0 kDa
Excluded volume excluded_volume	109570 Å³
Envelope volume envelope_volume	137780 Å³
Hydration-shell volume shell_volume	36314 Å³
Envelope diameter envelope_diameter	115.9 Å
Shell Rg shell_rg	38.10 Å
Envelope Rg envelope_rg	32.63 Å
Shape Rg shape_rg	32.68 Å
Total Rg total_rg	33.24 Å
Total atoms total_atoms	6165
Residues n_residues	806
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	109.2 Å
Rg (real space) rg_real	33.29 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.2230e+08
I(0) uncertainty (real space) i0_real_error	1.9870e+06
Rg (reciprocal space) rg_reciprocal	33.20 Å
I(0) (reciprocal space) i0_reciprocal	122300000.0000
Solution quality estimate total_estimate	0.8613
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.466
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22590000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.759

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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) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dkla_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

Domain ID domain_id	d1dklb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

CATH v4.4 (4 domains)

Domain ID domain_id	1dklA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	1dklA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	1dklB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	1dklB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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8. Citations (3)

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Unit-cell length a length_a	74.802 Å
Unit-cell length b length_b	72.126 Å
Unit-cell length c length_c	82.434 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.04 °
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	2.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1570
R_work r_work	0.1570
R_free r_free	0.2020

Description description	PHYTASE
Molecular weight formula_weight	44733.7 kDa
EC 编号 ec_number	3.1.3.2
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	6508

CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)

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

PHYTASE

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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

fit	/app/data/saxs_computation/dk/1dkl/1dkl.fit
pddf	/app/data/pr_computation/dk/1dkl/1dkl.pr.out
profile	/app/data/saxs_computation/dk/1dkl/1dkl.dat