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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

Method: X-RAY DIFFRACTION Dmax: 81.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHYTASE

Escherichia coli

UniProt P07102

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 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

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 1DKP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DKL CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND) 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）
Not recorded No recorded non-water small molecule 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
1DKL CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND) Deposited 1999-12-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–432（410 aa）
Not recorded No recorded non-water small molecule 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
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 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 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
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 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 7 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

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

SAXS profile for 1dkp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dkp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dkp
Deposition date deposition_date1999-12-08
Structure title titleCRYSTAL 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
Keywords keywordsHISTIDINE ACID PHOSPHATASE FOLD, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.64 Å
Radius of gyration Rg (electron density) rg_electron21.69 Å
Forward intensity I(0) i039853700.00
Molecular weight molecular_weight46112.0 kDa
Excluded volume excluded_volume56379 ų
Envelope volume envelope_volume65488 ų
Hydration-shell volume shell_volume24961 ų
Envelope diameter envelope_diameter83.5 Å
Shell Rg shell_rg28.87 Å
Envelope Rg envelope_rg22.22 Å
Shape Rg shape_rg21.73 Å
Total Rg total_rg22.37 Å
Total atoms total_atoms3180
Residues n_residues410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.7 Å
Rg (real space) rg_real22.63 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real3.9850e+07
I(0) uncertainty (real space) i0_real_error5.4760e+05
Rg (reciprocal space) rg_reciprocal22.63 Å
I(0) (reciprocal space) i0_reciprocal39850000.0000
Solution quality estimate total_estimate0.8397
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary80.5 Å
Skewness Skewness skewness0.416
Kurtosis Kurtosis kurtosis-0.019
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5403000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.646; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1dkpa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.2 — Histidine acid phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id1dkpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
Domain ID domain_id1dkpA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
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8. Citations (3)

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9. Files and Curves (10)