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1qlg

Crystal structure of phytase with magnesium from Bacillus amyloliquefaciens

Method: X-RAY DIFFRACTION Dmax: 62.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-PHYTASE

BACILLUS AMYLOLIQUEFACIENS

UniProt O66037

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 29–381 Not recorded CA CALCIUM ION × 3 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50 Resolution 2.20 Å R-free 0.265

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 1QLG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CVM CADMIUM INHIBITED CRYSTAL STRUCTURE OF PHYTASE FROM BACILLUS AMYLOLIQUEFACIENS Deposited 1999-08-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–381（353 aa）
Not recorded CA CALCIUM ION × 3 CD CADMIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10% MPD 0.1M MES pH 6.5 2mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.40 Å R-free 0.274
1H6L beta-propeller phytase in complex with phosphate and calcium ions Deposited 2001-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–381（353 aa）
Not recorded CA CALCIUM ION × 7 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 1.80 Å R-free 0.223
1POO THERMOSTABLE PHYTASE FROM BACILLUS SP Deposited 1999-04-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–383（355 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20% MPD, 0.1M MES (PH 6.5)
Resolution 2.10 Å R-free 0.291
2POO THERMOSTABLE PHYTASE IN FULLY CALCIUM LOADED STATE Deposited 1999-04-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–383（355 aa）
Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.05 Å R-free 0.262

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHYT_BACSP
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–353； UniProt 29–381

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 1qlg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1qlg
Deposition date deposition_date1999-08-31
Structure title titleCrystal structure of phytase with magnesium from Bacillus amyloliquefaciens
Keywords keywordsPHOSPHOMONOESTERASE, PHYTASE, THERMOSTABLE, PHOSPHATASE, CALCIUM, MAGNESIUM; PHOSPHOMONOESTERASE
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_guinier20.12 Å
Radius of gyration Rg (electron density) rg_electron18.90 Å
Forward intensity I(0) i027257400.00
Molecular weight molecular_weight38913.0 kDa
Excluded volume excluded_volume48093 ų
Envelope volume envelope_volume55056 ų
Hydration-shell volume shell_volume23296 ų
Envelope diameter envelope_diameter64.6 Å
Shell Rg shell_rg26.38 Å
Envelope Rg envelope_rg19.23 Å
Shape Rg shape_rg18.89 Å
Total Rg total_rg19.88 Å
Total atoms total_atoms2741
Residues n_residues353
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 dmax62.9 Å
Rg (real space) rg_real19.96 Å
Rg uncertainty (real space) rg_real_error0.22 Å
I(0) (real space) i0_real2.7260e+07
I(0) uncertainty (real space) i0_real_error2.8890e+05
Rg (reciprocal space) rg_reciprocal19.99 Å
I(0) (reciprocal space) i0_reciprocal27260000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.075
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9441000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.992
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1qlga_
Class classb — All beta proteins
Fold Fold foldb.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamilyb.68.3 — Thermostable phytase (3-phytase)
Family Family familyb.68.3.1 — Thermostable phytase (3-phytase)

CATH v4.4 (1 domains)

Domain ID domain_id1qlgA00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily30 — TolB, C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)