11tt

Crystal structure of apo alpha/beta-hydrolase macrolide esterase EstT from Sphingobacterium thalpophilum (S102A mutant)

Method: X-RAY DIFFRACTION D_max: 56.8 Å Quality: GOOD

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

alpha/beta-hydrolase macrolide esterase EstT

Sphingobacterium thalpophilum

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 1–287	Mutation：S102A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M Tris pH 9.6, 0.2 MgAc, 20% PEG 3350	Resolution 2.18 Å R-free 0.237

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	A0A4U9U5V9_9SPHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–287； UniProt 1–287

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	11tt
Deposition date deposition_date	2026-03-12
最后修订 last_revision	2026-04-08
Structure title title	Crystal structure of apo alpha/beta-hydrolase macrolide esterase EstT from Sphingobacterium thalpophilum (S102A mutant)
Keywords keywords	alpha/beta-hydrolase, esterase, macrolide resistance, 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	18.78 Å
Radius of gyration Rg (electron density) rg_electron	17.36 Å
Forward intensity I(0) i0	14893500.00
Molecular weight molecular_weight	28722.0 kDa
Excluded volume excluded_volume	35724 Å³
Envelope volume envelope_volume	40643 Å³
Hydration-shell volume shell_volume	19153 Å³
Envelope diameter envelope_diameter	57.0 Å
Shell Rg shell_rg	24.13 Å
Envelope Rg envelope_rg	17.53 Å
Shape Rg shape_rg	17.36 Å
Total Rg total_rg	18.34 Å
Total atoms total_atoms	2029
Residues n_residues	263
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	56.8 Å
Rg (real space) rg_real	18.62 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.4890e+07
I(0) uncertainty (real space) i0_real_error	1.6690e+05
Rg (reciprocal space) rg_reciprocal	18.65 Å
I(0) (reciprocal space) i0_reciprocal	14890000.0000
Solution quality estimate total_estimate	0.8983
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.044
Kurtosis Kurtosis kurtosis	-0.463
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3151000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.970

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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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8. Citations (1)

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Unit-cell length a length_a	46.778 Å
Unit-cell length b length_b	74.309 Å
Unit-cell length c length_c	77.004 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	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	29.090 Å
R factor r_factor	0.1894
R_work r_work	0.1838
R_free r_free	0.2375

Description description	alpha/beta-hydrolase macrolide esterase EstT
Molecular weight formula_weight	32405.5 kDa
EC 编号 ec_number	3.1.1.24
Mutation mutation	S102A
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2132

Crystal structure of apo alpha/beta-hydrolase macrolide esterase EstT from Sphingobacterium thalpophilum (S102A mutant)

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

alpha/beta-hydrolase macrolide esterase EstT

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Sphingobacterium thalpophilum
NCBI Class编号 ncbi_taxonomy_id	259
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

fit	/app/data/saxs_computation/1t/11tt/11tt.fit
pddf	/app/data/pr_computation/1t/11tt/11tt.pr.out
profile	/app/data/saxs_computation/1t/11tt/11tt.dat