7sdb

Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate

Method: X-RAY DIFFRACTION D_max: 63.0 Å Quality: GOOD

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

Myo-inositol phosphohydrolase

Legionella pneumophila str. Paris

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–319	Mutation：C231S	IHP INOSITOL HEXAKISPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；100 mM Tris HCl (7.4), 12% PEG 4000, 40 mM magnesium chloride	Resolution 2.00 Å R-free 0.199

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0AB38NCK8_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–320； UniProt 21–319

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	7sdb
Deposition date deposition_date	2021-09-29
Structure title title	Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate
Keywords keywords	Phytase, PTP fold, myo-inositol phosphate, effector protein, 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	19.70 Å
Radius of gyration Rg (electron density) rg_electron	18.95 Å
Forward intensity I(0) i0	20149600.00
Molecular weight molecular_weight	33748.0 kDa
Excluded volume excluded_volume	42024 Å³
Envelope volume envelope_volume	47241 Å³
Hydration-shell volume shell_volume	20611 Å³
Envelope diameter envelope_diameter	65.1 Å
Shell Rg shell_rg	25.47 Å
Envelope Rg envelope_rg	19.27 Å
Shape Rg shape_rg	18.92 Å
Total Rg total_rg	19.88 Å
Total atoms total_atoms	4610
Residues n_residues	288
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	63.0 Å
Rg (real space) rg_real	19.63 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.0150e+07
I(0) uncertainty (real space) i0_real_error	2.3630e+05
Rg (reciprocal space) rg_reciprocal	19.65 Å
I(0) (reciprocal space) i0_reciprocal	20150000.0000
Solution quality estimate total_estimate	0.8100
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.294
Kurtosis Kurtosis kurtosis	-0.273
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4134000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Myo-inositol phosphohydrolase
Molecular weight formula_weight	36387.1 kDa
Mutation mutation	C231S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5010

MGSSHHHHHHSSGLVPAGSHMSKLASSSVCDSTIENPCIVQDSKTQFSPVIRYREVASIADVYGGNITGINKFHLSGSEQPSEKGWEAIAESISRKMGPETKKVIVLDLRQESHGYLNGRAITLVSVYNWINLGKSNSQSTLDQENWLTGLRSRKIVNGVLTVPQYVAKQYSQGKSMVVSTVKNEEYYVYKKGFDYYRIFISDHRAPLDSEVDALVALIKNNPEDTWYHVHSRGGKGRTTTVFAMFDMLKNADKVSFEEIIARQASIPPFYNLMVTNREIPELTPYYEQRLQFLIHFYEFARQSLMGYSGTWSEWKKLNI

来源 Source

来源生物 organism	Legionella pneumophila str. Paris
NCBI Class编号 ncbi_taxonomy_id	297246
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	381

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8. Citations (1)

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Unit-cell length a length_a	62.309 Å
Unit-cell length b length_b	62.456 Å
Unit-cell length c length_c	95.497 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.080 Å
R factor r_factor	0.1636
R_work r_work	0.1605
R_free r_free	0.1990

fit	/app/data/saxs_computation/sd/7sdb/7sdb.fit
pddf	/app/data/pr_computation/sd/7sdb/7sdb.pr.out
profile	/app/data/saxs_computation/sd/7sdb/7sdb.dat